higlass / higlass-server Goto Github PK

Server component for HiGlass that manages and serves tiled data

License: MIT License

Python 81.99% Shell 0.99% Jupyter Notebook 16.59% Dockerfile 0.44%

higlass-server's Introduction

HiGlass Server

The HiGlass Server supports HiGlass and HiPiler by providing APIs for accessing and uploading tiles generated by Clodius.

Note: that the HiGlass Server itself only provides an API, and does not serve any HTML.

Installation

Prerequirements:

Python >=v3.6

Docker

The easiest way to run HiGlass with HiGlass Server is with Docker. More information is available at higlass-docker or check out the Dockerfile.

This project also includes a Dockerfile in the docker-context directory that can be used to run a locally checked out copy of higlass-server as follows:

docker build -t higlass-server -f docker-context/Dockerfile .
docker run -d --cap-add SYS_ADMIN --device /dev/fuse --security-opt apparmor:unconfined --name higlass-server higlass-server

Manually

To install HiGlass Server manually follow the steps below. Note we strongly recommend to create a virtual environment using Virtualenvwrapper for example. Skip step 2 if you don't work with virtual environments.

git clone https://github.com/higlass/higlass-server && cd higlass-server

Manually with virtualenvwrapper

mkvirtualenv -a $(pwd) -p $(which python3) higlass-server && workon higlass-server
pip install --upgrade -r ./requirements.txt
python manage.py migrate
python manage.py runserver

Manually with conda

conda env create -f environment.yml
conda activate higlass-server
python manage.py migrate
python manage.py runserver

To enable the register_url api endpoint, HiGlass depends on a project called httpfs to cache external url files. Tests depend on this process running. Set it up as follows:

pip install simple-httpfs

mkdir -p media/http
mkdir -p media/https
simple-httpfs media/http
simple-httpfs media/https

Or simply use ./unit_tests.sh.

Uploading Files

Although there is an API endpoint for uploading files, but it is more direct to use a manage.py script:

COOLER=dixon2012-h1hesc-hindiii-allreps-filtered.1000kb.multires.cool
HITILE=wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.hitile

wget -P data/ https://s3.amazonaws.com/pkerp/public/$COOLER
wget -P data/ https://s3.amazonaws.com/pkerp/public/$HITILE

python manage.py ingest_tileset --filename data/$COOLER --filetype cooler --datatype matrix --uid cooler-demo
python manage.py ingest_tileset --filename data/$HITILE --filetype hitile --datatype vector --uid hitile-demo

We can now use the API to get information about a tileset, or to get the tile data itself:

curl http://localhost:8000/api/v1/tileset_info/?d=hitile-demo
curl http://localhost:8000/api/v1/tiles/?d=hitile-demo.0.0.0

Development

Start the server:

python manage.py runserver localhost:8001
// or
npm start

Test the server:

./test.sh
// or
npm test

Bump version of server:

bumpversion patch

Update source code:

./update.sh

Troubleshooting

pybbi installation fails on macOS: Check out nvictus/pybbi#2

macOS 10.15 dependencies

brew install hdf5
brew install libpng
brew install jpeg
FUSE for Mac

License

The code in this repository is provided under the MIT License.

higlass-server's People

Contributors

Stargazers

Watchers

Forkers

jeewon-hwang msauria nvictus 4dn-dcic mildewey dlachowsky pkerpedjiev-zymergen alexpreynolds keller-mark ebirn astrovsky01 hms-dbmi cliffmeyer 101arrowz zhangzhen alexlenail robomics hzauleibowen

higlass-server's Issues

add sections on preparing other data types for use with HiGlass

We need to add sections to the README.md or to the wiki on how to convert BED and other important data formats for use with HiGlass:

BED
"2D BED"
what code to look at when having to create your own converter

link_tile returns a new uuid as a bytestring

When you register a Higlass file via /api/v/link_tile, the uuid is a byte string instead of an encoded string. In Python 3, it turns the uuid into an encoded string "b'<tileset_info>'", including the b''

I send this payload

{
'coordSystem': 'GRCh38', 
'filepath': '<AWS Bucket>/<Filename>.chrom.sizes', 
'filetype': 'chromsizes-tsv', 
'datatype': 'chromsizes'
}

res = requests.post(
                higlass_server + '/api/v1/link_tile/',
                data=json.dumps(payload),
                auth=authentication,
                headers=headers
            )

The server returns
{'uuid': "b'Cr1CSDnZSEqMW-Q2lM01Mw'"}

The uuid should be encoded to match the JSON response.

Admin page for ViewConf broken

Going to http://localhost:8000/admin/tilesets/viewconf/ results in error page saying that no such table: tilesets_viewconf. I've run all migrations but the table still seems to miss. Not sure why.

Migrations are not immutable

Related to #49. I checked the models and migration and notices that the ViewConf tables should have been created but Django kept telling me that all migrations have already been applied. The I checked the history of the migrations (https://github.com/hms-dbmi/higlass-server/blob/master/tilesets/migrations/0001_initial.py) and realized that they are not immutable. This is tricky as it makes updating existing server instances really painful.

Migrations should be immutable and instead new migrations should be added.

Make unit tests run independently without tests.sh wrapper.

Tests run when started using test.sh but not when running python manage.py test higlass_server. I guess this is because there needs to be some setup done first?

Would it be possible to make the unit tests independent?

fatal error: openssl/sha.h: No such file or directory

Just trying to install higlass-server

Here are my steps so far:

mkdir -p ~/work/github.com/hms-dbmi
cd ~/work/github.com/hms-dbmi

git clone [email protected]:hms-dbmi/higlass-server.git

cd higlass-server

conda create -n higlass-server python=3

conda install cython numpy

pip install --upgrade -r ./requirements.txt

Finally, I get:

udc.c:39:25: fatal error: openssl/sha.h: No such file or directory
    compilation terminated.

I guess I need to get the openssl dependency set up correctly... I'll post again if I find a fix.

I'm trying to compile on the Broad servers.

If you want the full error log, here it is:

  Running setup.py develop for pybbi
    Complete output from command /medpop/srlab/slowikow/miniconda2/envs/higlass-server/bin/python -c "import setuptools, tokenize;__file__='/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" develop --no-deps:
    Compiling /medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/bbi/cbbi.pyx because it depends on /medpop/srlab/slowikow/miniconda2/envs/higlass-server/lib/python3.6/site-packages/Cython/Includes/libc/stdlib.pxd.
    [1/1] Cythonizing /medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/bbi/cbbi.pyx
    running develop
    running egg_info
    writing pybbi.egg-info/PKG-INFO
    writing dependency_links to pybbi.egg-info/dependency_links.txt
    writing requirements to pybbi.egg-info/requires.txt
    writing top-level names to pybbi.egg-info/top_level.txt
    reading manifest file 'pybbi.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    warning: bbi/cbbi.pyx:542:8: Buffer unpacking not optimized away.
    warning: bbi/cbbi.pyx:542:8: Buffer unpacking not optimized away.
    warning: bbi/cbbi.pyx:594:8: Buffer unpacking not optimized away.
    warning: bbi/cbbi.pyx:594:8: Buffer unpacking not optimized away.
    warning: bbi/cbbi.pyx:622:23: local variable 'elements' referenced before assignment
    warning: bbi/cbbi.pyx:626:20: local variable 'elements' referenced before assignment
    warning: bbi/cbbi.pyx:630:20: local variable 'elements' referenced before assignment
    warning: bbi/cbbi.pyx:644:30: local variable 'elements' referenced before assignment
    warning: bbi/cbbi.pyx:661:20: local variable 'elements' referenced before assignment
    warning: no previously-included files matching '__pycache__/*' found anywhere in distribution
    warning: no previously-included files matching '*.o' found anywhere in distribution
    warning: no previously-included files matching '*.a' found anywhere in distribution
    warning: no previously-included files matching '*.so' found anywhere in distribution
    warning: no previously-included files matching '*.pyd' found anywhere in distribution
    warning: no previously-included files matching '*.pyc' found anywhere in distribution
    warning: no previously-included files matching '.git*' found anywhere in distribution
    warning: no previously-included files matching '.deps/*' found anywhere in distribution
    warning: no previously-included files matching '.DS_Store' found anywhere in distribution
    writing manifest file 'pybbi.egg-info/SOURCES.txt'
    running build_ext
    cd src && make
    make[1]: Entering directory `/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src'
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o aliType.o -c aliType.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o annoAssembly.o -c annoAssembly.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o annoFilter.o -c annoFilter.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o annoFormatter.o -c annoFormatter.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o annoFormatTab.o -c annoFormatTab.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o annoGrator.o -c annoGrator.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o annoGrateWig.o -c annoGrateWig.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o annoGratorQuery.o -c annoGratorQuery.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o annoOption.o -c annoOption.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o annoRow.o -c annoRow.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o annoStreamer.o -c annoStreamer.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o annoStreamBigBed.o -c annoStreamBigBed.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o annoStreamBigWig.o -c annoStreamBigWig.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o annoStreamTab.o -c annoStreamTab.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o annoStreamVcf.o -c annoStreamVcf.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o apacheLog.o -c apacheLog.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o asParse.o -c asParse.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o axt.o -c axt.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o axtAffine.o -c axtAffine.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o bamFile.o -c bamFile.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o base64.o -c base64.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o basicBed.o -c basicBed.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o bbiRead.o -c bbiRead.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o bbiWrite.o -c bbiWrite.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o bedTabix.o -c bedTabix.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o bigBed.o -c bigBed.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o binRange.o -c binRange.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o bits.o -c bits.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o blastOut.o -c blastOut.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o blastParse.o -c blastParse.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o boxClump.o -c boxClump.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o boxLump.o -c boxLump.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o bPlusTree.o -c bPlusTree.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o bwgCreate.o -c bwgCreate.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o bwgQuery.o -c bwgQuery.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o bwgValsOnChrom.o -c bwgValsOnChrom.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o cda.o -c cda.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o chain.o -c chain.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o chainBlock.o -c chainBlock.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o chainConnect.o -c chainConnect.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o chainToAxt.o -c chainToAxt.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o chainToPsl.o -c chainToPsl.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o cheapcgi.o -c cheapcgi.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o cirTree.o -c cirTree.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o codebias.o -c codebias.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o colHash.o -c colHash.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o common.o -c common.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o correlate.o -c correlate.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o crTree.o -c crTree.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o dgRange.o -c dgRange.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o diGraph.o -c diGraph.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o dlist.o -c dlist.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o dnaLoad.o -c dnaLoad.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o dnaMarkov.o -c dnaMarkov.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o dnaMotif.o -c dnaMotif.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o dnaseq.o -c dnaseq.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o dnautil.o -c dnautil.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o dtdParse.o -c dtdParse.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o dyOut.o -c dyOut.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o dystring.o -c dystring.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o elmTree.o -c elmTree.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o emblParse.o -c emblParse.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o errCatch.o -c errCatch.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o errAbort.o -c errAbort.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o fa.o -c fa.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o ffAli.o -c ffAli.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o ffScore.o -c ffScore.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o fieldedTable.o -c fieldedTable.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o filePath.o -c filePath.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o fixColor.o -c fixColor.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o flydna.o -c flydna.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o fof.o -c fof.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgCourier10.o -c font/mgCourier10.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgCourier12.o -c font/mgCourier12.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgCourier14.o -c font/mgCourier14.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgCourier18.o -c font/mgCourier18.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgCourier24.o -c font/mgCourier24.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgCourier34.o -c font/mgCourier34.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgCourier8.o -c font/mgCourier8.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgHelvetica10.o -c font/mgHelvetica10.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgHelvetica12.o -c font/mgHelvetica12.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgHelvetica14.o -c font/mgHelvetica14.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgHelvetica18.o -c font/mgHelvetica18.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgHelvetica24.o -c font/mgHelvetica24.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgHelvetica34.o -c font/mgHelvetica34.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgHelvetica8.o -c font/mgHelvetica8.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgHelveticaBold10.o -c font/mgHelveticaBold10.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgHelveticaBold12.o -c font/mgHelveticaBold12.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgHelveticaBold14.o -c font/mgHelveticaBold14.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgHelveticaBold18.o -c font/mgHelveticaBold18.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgHelveticaBold24.o -c font/mgHelveticaBold24.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgHelveticaBold34.o -c font/mgHelveticaBold34.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgHelveticaBold8.o -c font/mgHelveticaBold8.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgSixhi6.o -c font/mgSixhi6.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgSail8.o -c font/mgSail8.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgTimes10.o -c font/mgTimes10.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgTimes12.o -c font/mgTimes12.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgTimes14.o -c font/mgTimes14.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgTimes18.o -c font/mgTimes18.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgTimes24.o -c font/mgTimes24.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgTimes34.o -c font/mgTimes34.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgTimes8.o -c font/mgTimes8.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o font/mgMenlo12.o -c font/mgMenlo12.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o fq.o -c fq.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o fuzzyShow.o -c fuzzyShow.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o gapCalc.o -c gapCalc.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o gdf.o -c gdf.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o gemfont.o -c gemfont.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o genomeRangeTree.o -c genomeRangeTree.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o gfNet.o -c gfNet.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o gff.o -c gff.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o gff3.o -c gff3.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o gfxPoly.o -c gfxPoly.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o gifLabel.o -c gifLabel.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o hacTree.o -c hacTree.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o hash.o -c hash.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o hex.o -c hex.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o histogram.o -c histogram.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o hmmPfamParse.o -c hmmPfamParse.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o hmmstats.o -c hmmstats.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o htmlPage.o -c htmlPage.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o htmshell.o -c htmshell.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o hmac.o -c hmac.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o https.o -c https.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o intExp.o -c intExp.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o intValTree.o -c intValTree.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o internet.o -c internet.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o itsa.o -c itsa.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o iupac.o -c iupac.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o jointalign.o -c jointalign.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o jpegSize.o -c jpegSize.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o jsonParse.o -c jsonParse.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o jsonWrite.o -c jsonWrite.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o keys.o -c keys.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o knetUdc.o -c knetUdc.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o kxTok.o -c kxTok.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o linefile.o -c linefile.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o lineFileOnBigBed.o -c lineFileOnBigBed.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o localmem.o -c localmem.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o log.o -c log.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o longToList.o -c longToList.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o maf.o -c maf.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o mafFromAxt.o -c mafFromAxt.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o mafScore.o -c mafScore.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o mailViaPipe.o -c mailViaPipe.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o md5.o -c md5.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o memalloc.o -c memalloc.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o memgfx.o -c memgfx.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o meta.o -c meta.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o metaWig.o -c metaWig.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o mgCircle.o -c mgCircle.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o mgPolygon.o -c mgPolygon.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o mime.o -c mime.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o net.o -c net.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o nib.o -c nib.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o nibTwo.o -c nibTwo.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o nt4.o -c nt4.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o numObscure.o -c numObscure.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o obscure.o -c obscure.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o oldGff.o -c oldGff.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o oligoTm.o -c oligoTm.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o options.o -c options.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o osunix.o -c osunix.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o pairHmm.o -c pairHmm.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o pairDistance.o -c pairDistance.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o paraFetch.o -c paraFetch.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o peakCluster.o -c peakCluster.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o phyloTree.o -c phyloTree.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o pipeline.o -c pipeline.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o portimpl.o -c portimpl.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o pngwrite.o -c pngwrite.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o psGfx.o -c psGfx.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o psPoly.o -c psPoly.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o pscmGfx.o -c pscmGfx.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o psl.o -c psl.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o pslGenoShow.o -c pslGenoShow.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o pslShow.o -c pslShow.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o pslTbl.o -c pslTbl.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o pslTransMap.o -c pslTransMap.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o pthreadDoList.o -c pthreadDoList.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o pthreadWrap.o -c pthreadWrap.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o qa.o -c qa.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o quickHeap.o -c quickHeap.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o quotedP.o -c quotedP.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o ra.o -c ra.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o rainbow.o -c rainbow.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o raToStruct.o -c raToStruct.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o rbTree.o -c rbTree.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o rangeTree.o -c rangeTree.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o regexHelper.o -c regexHelper.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o repMask.o -c repMask.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o rle.o -c rle.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o rnautil.o -c rnautil.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o rqlEval.o -c rqlEval.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o rqlParse.o -c rqlParse.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o rudp.o -c rudp.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o scoreWindow.o -c scoreWindow.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o seg.o -c seg.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o seqOut.o -c seqOut.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o seqStats.o -c seqStats.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o servBrcMcw.o -c servBrcMcw.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o servCrunx.o -c servCrunx.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o servcis.o -c servcis.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o servcl.o -c servcl.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o servmsII.o -c servmsII.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o servpws.o -c servpws.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o shaRes.o -c shaRes.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o slog.o -c slog.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o snof.o -c snof.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o snofmake.o -c snofmake.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o snofsig.o -c snofsig.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o spaceSaver.o -c spaceSaver.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o spacedColumn.o -c spacedColumn.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o spacedSeed.o -c spacedSeed.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o splatAli.o -c splatAli.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o sqlList.o -c sqlList.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o sqlNum.o -c sqlNum.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o subText.o -c subText.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o sufa.o -c sufa.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o sufx.o -c sufx.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o synQueue.o -c synQueue.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o tabRow.o -c tabRow.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o tagStorm.o -c tagStorm.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o textOut.o -c textOut.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o tokenizer.o -c tokenizer.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o trix.o -c trix.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o twoBit.o -c twoBit.c
    gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/include -I/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src -I/usr/include -o udc.o -c udc.c
    udc.c:39:25: fatal error: openssl/sha.h: No such file or directory
    compilation terminated.
    make[1]: *** [udc.o] Error 1
    make[1]: Leaving directory `/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/src'
    make: *** [src/x86_64/libkent.a] Error 2
    Compiling libkent...
    LIBRARY_PATH: /broad/software/free/Linux/redhat_6_x86_64/pkgs/r_3.3.0/lib64:/broad/software/free/Linux/redhat_6_x86_64/pkgs/curl_7.47.1/lib:/broad/software/free/Linux/redhat_6_x86_64/pkgs/pcre_8.38/lib:/broad/software/free/Linux/redhat_6_x86_64/pkgs/xz_5.2.2/lib:/broad/software/free/Linux/redhat_6_x86_64/pkgs/zlib_1.2.6/lib64:/broad/software/free/Linux/redhat_6_x86_64/pkgs/bzip2_1.0.6/lib:/broad/software/free/Linux/redhat_6_x86_64/pkgs/libiconv_1.13.1/lib:/broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.2.0/lib64:/broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.2.0/lib:/broad/software/free/Linux/redhat_6_x86_64/pkgs/netcdf_4.3.3.1/lib:/broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_4.9.0/lib64:/broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_4.9.0/lib:/broad/software/free/Linux/redhat_6_x86_64/pkgs/ruby_2.0.0-p451/lib:/broad/software/free/Linux/redhat_6_x86_64/pkgs/vim_7.4/lib:/broad/software/free/Linux/redhat_6_x86_64/pkgs/jdk1.8.0_121/lib:/broad/software/free/Linux/redhat_6_x86_64/pkgs/cmake_2.8.11.2/lib:/broad/software/free/Linux/redhat_6_x86_64/pkgs/automake_1.12.5/lib:/broad/software/free/Linux/redhat_6_x86_64/pkgs/perl_5.18.1/lib:/broad/software/free/Linux/redhat_6_x86_64/pkgs/git_2.5.0/lib:/broad/software/free/Linux/redhat_6_x86_64/pkgs/pigz_2.1.6/lib:/broad/software/free/Linux/redhat_6_x86_64/pkgs/imagemagick_6.9.0-5/lib:/broad/software/free/Linux/redhat_6_x86_64/pkgs/libevent_2.0.16-stable/lib:/home/unix/slowikow/.linuxbrew/lib
    C_INCLUDE_PATH: /medpop/srlab/slowikow/miniconda2/envs/higlass-server/include/openssl:/broad/software/free/Linux/redhat_6_x86_64/pkgs/curl_7.47.1/include:/broad/software/free/Linux/redhat_6_x86_64/pkgs/pcre_8.38/include:/broad/software/free/Linux/redhat_6_x86_64/pkgs/xz_5.2.2/include:/broad/software/free/Linux/redhat_6_x86_64/pkgs/zlib_1.2.6/include:/broad/software/free/Linux/redhat_6_x86_64/pkgs/bzip2_1.0.6/include:/broad/software/free/Linux/redhat_6_x86_64/pkgs/libiconv_1.13.1/include:/broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_5.2.0/include:/broad/software/free/Linux/redhat_6_x86_64/pkgs/netcdf_4.3.3.1/include:/broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_4.9.0/include:/broad/software/free/Linux/redhat_6_x86_64/pkgs/ruby_2.0.0-p451/include:/broad/software/free/Linux/redhat_6_x86_64/pkgs/vim_7.4/include:/broad/software/free/Linux/redhat_6_x86_64/pkgs/jdk1.8.0_121/include:/broad/software/free/Linux/redhat_6_x86_64/pkgs/cmake_2.8.11.2/include:/broad/software/free/Linux/redhat_6_x86_64/pkgs/automake_1.12.5/include:/broad/software/free/Linux/redhat_6_x86_64/pkgs/perl_5.18.1/include:/broad/software/free/Linux/redhat_6_x86_64/pkgs/git_2.5.0/include:/broad/software/free/Linux/redhat_6_x86_64/pkgs/pigz_2.1.6/include:/broad/software/free/Linux/redhat_6_x86_64/pkgs/imagemagick_6.9.0-5/include:/broad/software/free/Linux/redhat_6_x86_64/pkgs/libevent_2.0.16-stable/include
    Traceback (most recent call last):
      File "", line 1, in 
      File "/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/setup.py", line 97, in 
        'build_ext': build_ext
      File "/medpop/srlab/slowikow/miniconda2/envs/higlass-server/lib/python3.6/site-packages/setuptools/__init__.py", line 129, in setup
        return distutils.core.setup(**attrs)
      File "/medpop/srlab/slowikow/miniconda2/envs/higlass-server/lib/python3.6/distutils/core.py", line 148, in setup
        dist.run_commands()
      File "/medpop/srlab/slowikow/miniconda2/envs/higlass-server/lib/python3.6/distutils/dist.py", line 955, in run_commands
        self.run_command(cmd)
      File "/medpop/srlab/slowikow/miniconda2/envs/higlass-server/lib/python3.6/distutils/dist.py", line 974, in run_command
        cmd_obj.run()
      File "/medpop/srlab/slowikow/miniconda2/envs/higlass-server/lib/python3.6/site-packages/setuptools/command/develop.py", line 36, in run
        self.install_for_development()
      File "/medpop/srlab/slowikow/miniconda2/envs/higlass-server/lib/python3.6/site-packages/setuptools/command/develop.py", line 136, in install_for_development
        self.run_command('build_ext')
      File "/medpop/srlab/slowikow/miniconda2/envs/higlass-server/lib/python3.6/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/medpop/srlab/slowikow/miniconda2/envs/higlass-server/lib/python3.6/distutils/dist.py", line 974, in run_command
        cmd_obj.run()
      File "/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/setup.py", line 47, in run
        check_call(['make', 'build-c'])
      File "/medpop/srlab/slowikow/miniconda2/envs/higlass-server/lib/python3.6/subprocess.py", line 291, in check_call
        raise CalledProcessError(retcode, cmd)
    subprocess.CalledProcessError: Command '['make', 'build-c']' returned non-zero exit status 2.
----------------------------------------

Command "/medpop/srlab/slowikow/miniconda2/envs/higlass-server/bin/python -c "import setuptools, tokenize;file='/medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" develop --no-deps" failed with error code 1 in /medpop/srlab/slowikow/work/github.com/hms-dbmi/higlass-server/src/pybbi/

Fix test cooler file

The file at https://s3.amazonaws.com/pkerp/public/dixon2012-h1hesc-hindiii-allreps-filtered.1000kb.multires.cool does not contain necessary attributes, such as max_zoom. It should be replaced by data/dixon2012-h1hesc-hindiii-allreps-filtered.1000kb.multires.cool.

The AWS files only contains the following attrs:

while the checked in file additionally has:

4
max_zoom

Gene suggestions for 'Clock' yields Per2

(hg-server) ===========================================================================================================
[peter@mbi-cw-l10381 higlass-server] [master]$ python
Python 2.7.11 (default, Nov 17 2016, 17:37:33)
[GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.42.1)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import tilesets.suggestions as ts
>>> ts.get_gene_suggestions('data/gene-annotations-mm9.db', 'Clock')
[{'chr': u'chr1', 'score': 394.0, 'geneName': u'Per2', 'txEnd': 93355905, 'txStart': 93312558}, {'chr': u'chr5', 'score': 308.0, 'geneName': u'Clock', 'txEnd': 76733817, 'txStart': 76638892}, {'chr': u'chr11', 'score': 283.0, 'geneName': u'Per1', 'txEnd': 68923459, 'txStart': 68912457}, {'chr': u'chr4', 'score': 69.0, 'geneName': u'Per3', 'txEnd': 150418774, 'txStart': 150377763}, {'chr': u'chr10', 'score': 41.0, 'geneName': u'Timeless', 'txEnd': 127689997, 'txStart': 127669118}, {'chr': u'chr12', 'score': 19.0, 'geneName': u'Cipc', 'txEnd': 88306316, 'txStart': 88287990}]

Server returns 500 for unknown tileset uuids when pulling tiles

The following line https://github.com/hms-dbmi/higlass-server/blob/master/tilesets/views.py#L396 does not catch tilesets.models.DoesNotExist.

Can't read tiles for dm5 gene annotations

Error:

----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/peter/projects/higlass-server/tilesets/tests.py", line 41, in test_to_string
    tile = json.loads(self.client.get('/api/v1/tiles/?d=ga1.0.0').content)
  File "/Users/peter/.virtualenvs/hg-server/lib/python2.7/site-packages/django/test/client.py", line 529, in get
    **extra)
  File "/Users/peter/.virtualenvs/hg-server/lib/python2.7/site-packages/django/test/client.py", line 333, in get
    return self.generic('GET', path, secure=secure, **r)
  File "/Users/peter/.virtualenvs/hg-server/lib/python2.7/site-packages/django/test/client.py", line 409, in generic
    return self.request(**r)
  File "/Users/peter/.virtualenvs/hg-server/lib/python2.7/site-packages/django/test/client.py", line 494, in request
    six.reraise(*exc_info)
  File "/Users/peter/.virtualenvs/hg-server/lib/python2.7/site-packages/django/core/handlers/exception.py", line 39, in inner
    response = get_response(request)
  File "/Users/peter/.virtualenvs/hg-server/lib/python2.7/site-packages/django/core/handlers/base.py", line 187, in _get_response
    response = self.process_exception_by_middleware(e, request)
  File "/Users/peter/.virtualenvs/hg-server/lib/python2.7/site-packages/django/core/handlers/base.py", line 185, in _get_response
    response = wrapped_callback(request, *callback_args, **callback_kwargs)
  File "/Users/peter/.virtualenvs/hg-server/lib/python2.7/site-packages/django/views/decorators/csrf.py", line 58, in wrapped_view
    return view_func(*args, **kwargs)
  File "/Users/peter/.virtualenvs/hg-server/lib/python2.7/site-packages/django/views/generic/base.py", line 68, in view
    return self.dispatch(request, *args, **kwargs)
  File "/Users/peter/.virtualenvs/hg-server/lib/python2.7/site-packages/rest_framework/views.py", line 474, in dispatch
    response = self.handle_exception(exc)
  File "/Users/peter/.virtualenvs/hg-server/lib/python2.7/site-packages/rest_framework/views.py", line 434, in handle_exception
    self.raise_uncaught_exception(exc)
  File "/Users/peter/.virtualenvs/hg-server/lib/python2.7/site-packages/rest_framework/views.py", line 471, in dispatch
    response = handler(request, *args, **kwargs)
  File "/Users/peter/.virtualenvs/hg-server/lib/python2.7/site-packages/rest_framework/decorators.py", line 52, in handler
    return func(*args, **kwargs)
  File "/Users/peter/projects/higlass-server/tilesets/views.py", line 303, in tiles
    res = map(lambda x: generate_tile(x, request), tileids_to_fetch)
  File "/Users/peter/projects/higlass-server/tilesets/views.py", line 303, in <lambda>
    res = map(lambda x: generate_tile(x, request), tileids_to_fetch)
  File "/Users/peter/projects/higlass-server/tilesets/views.py", line 210, in generate_tile
    rdb.set(tile_id, pickle.dumps(tile_value))
  File "/Users/peter/.virtualenvs/hg-server/bin/../lib/python2.7/copy_reg.py", line 70, in _reduce_ex
    raise TypeError, "can't pickle %s objects" % base.__name__
TypeError: can't pickle buffer objects

ingest_tileset probably does not work with ftp

higlass-server/tilesets/management/commands/ingest_tileset.py

Line 34 in 5a189e2

if filename[:8] == 'ftp://':

This will never evaluate to True: The character count is wrong.
startswith would be better... or the three if-thens could be replaced with a single regex.

chromsizes file is not properly ingested into server database

Hi,

I have installed higlass server 1.7.3 from github and the client v1.3.1 (I cannot use docker at my infrastructure). (Actually, it were the latest git checkouts from Feb. 1st 2019. The version numbers in the changelogs seem not to follow the release version numbers).

I have ingested a chromsizes file and a genome annotation file for hg19 by
python manage.py ingest_tileset --filename chromSizes.tsv --filetype chromsizes-tsv --datatype chromsizes --coordSystem hg19 --name "Chromosomes (hg19)" --uid chromSizes-hg19 --coordSystem2 hg19

and

python manage.py ingest_tileset --filename gene-annotations-hg19.beddb --filetype beddb --datatype gene-annotation --coordSystem hg19 --name anno_hg19 --uid anno_hg19

However when running client and trying to use the search bar I am not even getting hg19 as a putative species for selection. The dubugger clearly states that it tries to access
/api/v1/chrom-sizes/ which does not exist likely due to a faulty ingestion procedure. Do you have an idea how to solve it?

Cheers

Raises an exception when the file is corrupted

https://github.com/hms-dbmi/higlass-server/blob/b1078cbb6a4aec10ad6c7f18cbfc52e66686da0e/tilesets/views.py#L548-L550

Reproduce:

remove all uploaded files
see it break

AWS-related tests appear to fail

I'm curious if the slashes in an AWS URL are setting up non-existent paths in the media directory.

From the develop branch:

(higlass-server) $ ./test.sh
...
(higlass-server) $ python manage.py test tilesets
.[E::hts_open_format] Failed to open file /home/ubuntu/higlass-server/media/https/s3.amazonaws.com/pkerp/public/SRR1770413.sorted.short.bam..
E.....................F................................
======================================================================
ERROR: test_register_bam_url (tilesets.tests.BamTests)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/ubuntu/higlass-server/tilesets/tests.py", line 425, in test_register_bam_url
    response = c.get(f'/api/v1/tileset_info/?d={uid}')
  File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/django/test/client.py", line 527, in get
    response = super().get(path, data=data, secure=secure, **extra)
  File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/django/test/client.py", line 339, in get
    **extra,
  File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/django/test/client.py", line 414, in generic
    return self.request(**r)
  File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/django/test/client.py", line 495, in request
    raise exc_value
  File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/django/core/handlers/exception.py", line 34, in inner
    response = get_response(request)
  File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/django/core/handlers/base.py", line 126, in _get_response
    response = self.process_exception_by_middleware(e, request)
  File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/django/core/handlers/base.py", line 124, in _get_response
    response = wrapped_callback(request, *callback_args, **callback_kwargs)
  File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/django/views/decorators/csrf.py", line 54, in wrapped_view
    return view_func(*args, **kwargs)
  File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/django/views/generic/base.py", line 68, in view
    return self.dispatch(request, *args, **kwargs)
  File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/rest_framework/views.py", line 495, in dispatch
    response = self.handle_exception(exc)
  File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/rest_framework/views.py", line 455, in handle_exception
    self.raise_uncaught_exception(exc)
  File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/rest_framework/views.py", line 492, in dispatch
    response = handler(request, *args, **kwargs)
  File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/rest_framework/decorators.py", line 54, in handler
    return func(*args, **kwargs)
  File "/home/ubuntu/higlass-server/tilesets/views.py", line 628, in tileset_info
    tileset_object.datafile.path
  File "/home/ubuntu/clodius/clodius/tiles/bam.py", line 124, in tileset_info
    samfile = pysam.AlignmentFile(filename)
  File "pysam/libcalignmentfile.pyx", line 736, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 935, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/home/ubuntu/higlass-server/media/https/s3.amazonaws.com/pkerp/public/SRR1770413.sorted.short.bam..`: No such file or directory

======================================================================
FAIL: test_register_url (tilesets.tests.FileUploadTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/ubuntu/higlass-server/tilesets/tests.py", line 1322, in test_register_url
    self.assertEqual(200, response.status_code, response.content)
AssertionError: 200 != 500 : b'{"error": "File not found: /home/ubuntu/higlass-server/media/https/s3.amazonaws.com/pkerp/public/wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.bigWig.."}'

----------------------------------------------------------------------
Ran 56 tests in 29.742s

FAILED (failures=1, errors=1)
Creating test database for alias 'default'...
System check identified no issues (0 silenced).
No coordinate system specified, but we found matching chromsizes. Using coordinate system hg19_1.
Using coordinates for coordinate system: hg19_r
No coordinate system specified, but we found matching chromsizes. Using coordinate system hg19_1.
Destroying test database for alias 'default'...

Document dependencies to build from scratch?

Having trouble with my local environment, so tried to start it within a container. These were the steps... not sure if this would be worth documenting?

docker run -dit --name ubuntu-container ubuntu
docker exec -it ubuntu-container /bin/bash

and then:

cd ~
apt-get update
apt-get install libatlas-dev libatlas-base-dev liblapack-dev gfortran wget bzip2 git libz-dev curl
wget http://repo.continuum.io/miniconda/Miniconda2-4.2.12-Linux-x86_64.sh -O miniconda.sh
bash miniconda.sh -b -p $HOME/miniconda
export PATH="$HOME/miniconda/bin:$PATH"
conda install --yes python=2.7.12 cython==0.25.2 numpy=1.11.2
git clone https://github.com/hms-dbmi/higlass-server.git
cd higlass-server/
pip install -r requirements.txt
pip install -r requirements-secondary.txt
python manage.py migrate
./test.sh

Is it 'uid' or 'uuid'?

In some places it's one, in some places another. I remember Nils having concerns that if the user can assign it, it's not really universally unique, so maybe that's why it's only one "u" in some places? I don't care, and would be happy with any of uuid/uid/id, but the inconsistency seems like something we'll trip over in the future.

Adding track using fileURL to viewConfig gives error

I'm trying to follow the instructions for adding tracks using the viewConfig. There is a section about adding tracks using a fileURL:

https://docs.higlass.io/view_config.html#tracks

When I try to follow the example given in the docs, I get in the higlass browser: "Unknown track type: vector". If I change the type in the viewConfig to horizontal-line, I only get "Loading..." in the browser. Here's my viewConfig:

{
"editable": true,
"zoomFixed": false,
"trackSourceServers": [
"/api/v1",
"http://higlass.io/api/v1"
],
"exportViewUrl": "/api/v1/viewconfs/",
"views": [
{
"tracks": {
"top": [
{
"type": "horizontal-line",
"server": "http://higlass.io/api/v1",
"fileUrl": "http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878InputStdSig.bigWig",
"height": 20,
"uid": "P7PStqTERwSQIYfuiag7Pg",
"options": {
"labelColor": "black",
"labelPosition": "topLeft",
"labelLeftMargin": 0,
"labelRightMargin": 0,
"labelTopMargin": 0,
"labelBottomMargin": 0,
"labelBackgroundColor": "white",
"labelShowResolution": false,
"axisLabelFormatting": "scientific",
"axisPositionHorizontal": "right",
"lineStrokeColor": "blue",
"lineStrokeWidth": 1,
"valueScaling": "linear",
"trackBorderWidth": 0,
"trackBorderColor": "black",
"labelTextOpacity": 0.4,
"showMousePosition": false,
"mousePositionColor": "#000000",
"showTooltip": false
}
}
],
"left": [],
"center": [],
"right": [],
"bottom": [],
"whole": [],
"gallery": []
},
"initialXDomain": [
804790556.208501,
2395846923.287899
],
"initialYDomain": [
409150616.7513812,
2792349941.057543
],
"layout": {
"w": 12,
"h": 12,
"x": 0,
"y": 0,
"moved": false,
"static": false
},
"uid": "RdhK3CqOSBOQdROn7DzJkQ"
}
],
"zoomLocks": {
"locksByViewUid": {},
"locksDict": {}
},
"locationLocks": {
"locksByViewUid": {},
"locksDict": {}
},
"valueScaleLocks": {
"locksByViewUid": {},
"locksDict": {}
}
}

Looking in the browser console, I see the following error:

Failed to load resource: the server responded with a status of 500 (Internal Server Error) higlass.io/api/v1/register_url/:1

Error registering url TypeError: Cannot read property 'chromsizes' of null
at hglib.min.js:1
at e. (hglib.min.js:8)
at hglib.min.js:8

Any idea what I'm doing wrong? Thanks in advance.

Tileset info request should not return the `datafile` field

          {
            "datafile": "http://localhost:8989/api/v1/tilesets/media/uploads/bedpe_mOTjjJ2.db",
            "name": "bedpe.db",
            "server": "http://localhost:8989/api/v1",
            "tilesetUid": "cVy8NEbxSoijEqpH0XnK-g",
            "uid": "E0tHFp2UTJ6IkSLlVyWrnQ",
            "type": "horizontal-2d-rectangle-domains",
            "options": {
              "labelColor": "black",
              "labelPosition": "hidden",
              "name": "bedpe.db"
            },
            "width": 908,
            "height": 178,
            "position": "top"
          }

Probably related to this line in higlass_server:

        #ts_serializer = tss.UserFacingTilesetSerializer(queryset, many=True)
        page = self.paginate_queryset(queryset)
        if page is not None:
            serializer = self.get_serializer(page, many=True)
            return self.get_paginated_response(serializer.data)

Django does not display CSS, JS, or images

I'm trying to follow your steps to get higlass-server running. Could I ask if you have any advice to get this working correctly? I think I'm almost there, but something is missing because the assets like JS and CSS are not loading.

I installed like this:

mkdir -p ~/work/github.com/hms-dbmi
cd ~/work/github.com/hms-dbmi

git clone [email protected]:hms-dbmi/higlass-server.git

cd higlass-server

conda create -n higlass-server python=3

conda install cython numpy

pip install --upgrade -r ./requirements.txt
pip install --upgrade -r ./requirements-secondary.txt

Then I tried running:

COOLER=dixon2012-h1hesc-hindiii-allreps-filtered.1000kb.multires.cool

wget -P data/ https://s3.amazonaws.com/pkerp/public/$COOLER

python manage.py ingest_tileset --filename data/$COOLER --filetype cooler --datatype matrix --uid cooler-demo

python manage.py runserver

Performing system checks...

/medpop/srlab/slowikow/miniconda2/envs/higlass-server/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
System check identified no issues (0 silenced).
March 07, 2018 - 02:09:51
Django version 2.0, using settings 'higlass_server.settings'
Starting development server at http://127.0.0.1:8000/
Quit the server with CONTROL-C.

At this point I start a tunnel from my laptop to the server:

ssh -N -L 8000:localhost:8000 server

But now the page does not load correctly in my browser on my laptop. I get this in my console when I visit http://localhost:8000/admin

GET http://localhost:8000/hgs-static/admin/css/responsive.css net::ERR_ABORTED
localhost/:6 GET http://localhost:8000/hgs-static/admin/css/base.css net::ERR_ABORTED
localhost/:7 GET http://localhost:8000/hgs-static/admin/css/dashboard.css net::ERR_ABORTED

I can login to the admin console and see some of the HTML, but it is missing all of the assets like CSS.

/api/v1/viewconfs/ 500 error when the post body is empty

Empty post requests to /api/v1/viewconfs/ lead to an internal 500 error instead of a 400 error.

unused variable "datatype"?

my IDE is pointing out that datatype is never used, and so this whole block has no real effect, I think?:

datatype = None
if 'datatype' not in self.request.data:
  if self.request.data['filetype'] == 'cooler':
    datatype = 'matrix'
  elif self.request.data['filetype'] == 'hitile':
    datatype = 'vector'
  else:
    raise rfe.APIException('Missing datatype. Could not infer from filetype:', self.request.data['filetype'])

Not sure whether it's vestigial, or if that field should be used? Also, do you have strong feelings about static code analysis tools? Refinery is using flake8, I think.

get rid of test.sh

Different tests have different setup requirements. End goal is to only have python tests and call them via manage.

Chromosome sizes should be stored in the tilesets table

We don't need a separate table to store chromosome sizes. This will make it easier to create and select new chromosome axes.

Tests keep re-downloading the same files

When running ./tests.sh the same set of tests files (which are kind of large) are re-downloaded instead of re-used. Since the tasks is not to test the internet connection the tests should first check if the test files are actually available.

Secret key on GitHub

Currently the secret key is stored publicly in settings.py. Since most people won't know that they have to change it. Maybe the approach from Refinery can be reused (i.e., reading a config json that has to be created manually or could be created automatically)

4xx instead of 5xx for bad API calls

There are a range of situations where the API returns an 500 response where a 4xx would be more appropriate.

Try to reassign an existing ID
Try to fetch a viewconf which does not exist

DB Errors are being thrown internally and we don't catch them. We want to catch these and handle them correctly.

(I think we do not want to do pre-flight queries: that would be vulnerable to race conditions.)

Do pre-flight check for conflicting UIDs

The database update happens at the end of an ingest. Particularly with large files this can be annoying: I up-arrow to rerun a command from the history, and it's only at the end when it tries to ingest it into the database that I get an error because of the reused ID.

Simplest fix would be to query the database at the very start, if the user has given an ID.
Or, slightly more sophisticated: add a placeholder record at the start of the script, and then update that at the end. This would be more robust against race conditions, but not sure if it's worth the complexity.

$ docker exec higlass-container python higlass-server/manage.py ingest_tileset --filename /tmp/$COOLER --filetype cooler --datatype matrix --uid $ID
Traceback (most recent call last):
...
  File "/home/higlass/projects/higlass-server/tilesets/management/commands/ingest_tileset.py", line 35, in handle
    name=name)
...
    return Database.Cursor.execute(self, query, params)
django.db.utils.IntegrityError: UNIQUE constraint failed: tilesets_tileset.uuid

Trouble GETting a viewconf I've POSTed

On the 0.0.7 Docker image: (or from source: I just replicated it)

$ curl --form 'fileupload={"foo":"bar"}' http://localhost:8888/api/v1/viewconfs/
{"uid": "WsQUwinvSe2LE09eRi0vxA"}

$ curl http://localhost:8888/api/v1/viewconfs/?d=WsQUwinvSe2LE09eRi0vxA
<h1>Server Error (500)</h1>

Should it require username and password?
Could the ID be set on the post? Would make it a little bit easier to script, rather than parsing the JSON? But it's reasonable not to offer that, too.
Why doesn't the GET work?

POST causes no error in the log, but on the GET:

[13/Feb/2017 21:08:17] ERROR [django.request:124] Internal Server Error: /api/v1/viewconfs/
Traceback (most recent call last):
  File "/opt/conda/lib/python2.7/site-packages/django/core/handlers/exception.py", line 39, in inner
    response = get_response(request)
  File "/opt/conda/lib/python2.7/site-packages/django/core/handlers/base.py", line 187, in _get_response
    response = self.process_exception_by_middleware(e, request)
  File "/opt/conda/lib/python2.7/site-packages/django/core/handlers/base.py", line 185, in _get_response
    response = wrapped_callback(request, *callback_args, **callback_kwargs)
  File "/opt/conda/lib/python2.7/site-packages/django/views/decorators/csrf.py", line 58, in wrapped_view
    return view_func(*args, **kwargs)
  File "/opt/conda/lib/python2.7/site-packages/django/views/generic/base.py", line 68, in view
    return self.dispatch(request, *args, **kwargs)
  File "/opt/conda/lib/python2.7/site-packages/rest_framework/views.py", line 477, in dispatch
    response = self.handle_exception(exc)
  File "/opt/conda/lib/python2.7/site-packages/rest_framework/views.py", line 437, in handle_exception
    self.raise_uncaught_exception(exc)
  File "/opt/conda/lib/python2.7/site-packages/rest_framework/views.py", line 474, in dispatch
    response = handler(request, *args, **kwargs)
  File "/opt/conda/lib/python2.7/site-packages/rest_framework/decorators.py", line 52, in handler
    return func(*args, **kwargs)
  File "./tilesets/views.py", line 254, in viewconfs
    return JsonResponse(json.loads(obj.viewconf))
  File "/opt/conda/lib/python2.7/json/__init__.py", line 339, in loads
    return _default_decoder.decode(s)
  File "/opt/conda/lib/python2.7/json/decoder.py", line 364, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/opt/conda/lib/python2.7/json/decoder.py", line 382, in raw_decode
    raise ValueError("No JSON object could be decoded")
ValueError: No JSON object could be decoded

Maybe it's not actually writing to the database?

Make APIs more consistent / use ViewSet subclasses?

I'm copy-and-pasting the the bit to make ID assignable, but it feels like there is a lot of overlap between the two, and an abstract superclass might be appropriate?

Unit tests in readme.md failing

I think it's just more wgets needed in the readme... perhaps move this setup inside the test, and have it run on Travis.

======================================================================
ERROR: test_get_tile (tilesets.tests.BedDBTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/chuck/github/hms-dbmi/higlass-server/tilesets/tests.py", line 97, in setUp
    upload_file = open('data/gene_annotations.short.db', 'r')
IOError: [Errno 2] No such file or directory: 'data/gene_annotations.short.db'

======================================================================
ERROR: test_upload_file (tilesets.tests.FileUploadTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/chuck/github/hms-dbmi/higlass-server/tilesets/tests.py", line 60, in test_upload_file
    f = open( 'data/tiny.txt', 'r')
IOError: [Errno 2] No such file or directory: 'data/tiny.txt'

======================================================================
ERROR: test_hibed_get_tile (tilesets.tests.HiBedTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/chuck/github/hms-dbmi/higlass-server/tilesets/tests.py", line 122, in setUp
    upload_file = open('data/cnv_short.hibed', 'r')
IOError: [Errno 2] No such file or directory: 'data/cnv_short.hibed'

======================================================================
ERROR: test_hibed_get_tileset_info (tilesets.tests.HiBedTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/chuck/github/hms-dbmi/higlass-server/tilesets/tests.py", line 122, in setUp
    upload_file = open('data/cnv_short.hibed', 'r')
IOError: [Errno 2] No such file or directory: 'data/cnv_short.hibed'

======================================================================
ERROR: test_suggest (tilesets.tests.SuggestionsTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/chuck/github/hms-dbmi/higlass-server/tilesets/tests.py", line 28, in setUp
    upload_file = open('data/gene_annotations.short.db', 'r')
IOError: [Errno 2] No such file or directory: 'data/gene_annotations.short.db'

----------------------------------------------------------------------
Ran 20 tests in 11.035s

Cannot delete tileset using uuid through REST api

Given a tileset with uuid sim_02_sorted.ballele

The following call to the rest interface returns an error and does not delete the tileset:
DELETE .../api/v1/tilesets/sim_02_sorted.ballele

<h1>Not Found</h1>
<p>The requested URL /api/v1/tilesets/sim_02_sorted.ballele/ was not found on this server.</p>

cooler vs clodius

The requirements.txt file specifies a fixed version of cooler (0.7.11), but indicates clodius>=0.10.3. This results in the following warning:

ERROR: clodius 0.10.8 has requirement cooler>=0.8.0, but you'll have cooler 0.7.11 which is incompatible.

Would it not be safer to use pip freeze to fix all versions at a known good version for the release?

Don't know how to / Can't assign UID when uploading

Sorry if this something simple I'm missing:

set -x
set -v

VIEWCONF='{}'
VIEWCONF_UID=empty-view
VIEWCONFS_URL=http://localhost:8888/api/v1/viewconfs/

# This doesn't work: Trying to curl in two different incompatible ways.
curl --globoff -H "Content-Type: application/json" -X POST -d "$VIEWCONF" $VIEWCONFS_URL -F "uid=$VIEWCONF_UID"

# Not recognized as a parameter in the url: random UID still generated. (GET will work.)
curl --globoff -H "Content-Type: application/json" -X POST -d "$VIEWCONF" $VIEWCONFS_URL'?uid='$VIEWCONF_UID

# UID is not recognized, and the data stored in the database has HTTP cruft. (GET fails because JSON can't be parsed.)
curl --globoff -F "fileupload=$VIEWCONF" -F "uid=$VIEWCONF_UID" $VIEWCONFS_URL

echo

Uids with the '.' character throw off the tiling logic.

The tiling logic is hard coded to split a field containing the uid and take [1:3]. If the uid includes a '.' character, the tiling logic is broken by this case.

Installation errors

This issue is to document the errors I got when installing the requirements and how they were fixed.

Either libcurl isn't installed, it didn't come with curl-config, or curl-config isn't in your $PATH. This must be corrected before installing pyBigWig!

Fixed with sudo apt-get install libcurl4-gnutls-dev

#include "png.h"   // MUST come before common.h, due to setjmp checking  in pngconf.h

Fixed with sudo apt-get install libpng-dev

Document and/or test API via curl

It would be good to have examples of API usage via curl, either in the docs, or tests: I'd slightly prefer tests to be the priority. (Motivated by #13.)

POST tileset
POST tileset with preset UID
POST tileset, invalid? (What happens if the parameters are set wrong? When is that caught?)
GET tileset
GET non-existent tileset
POST viewconf
POST viewconf with preset UID
POST viewconf, invalid JSON, and get error
GET viewconf
GET non-existent viewconf

README: What is </path/to/data>

Following the readme, I'm not sure what to do at this point.... Should I have already created </path/to/data>/https and </path/to/data>/http?

git clone https://github.com/reservoirgenomics/httpfs.git
pip install -r httpfs/requirements.txt
python /internal-services/httpfs/httpfs.py </path/to/data>/https https --lru-capacity 1000 --disk-cache-dir /data/disk-cache --disk-cache-size 4294967296
python /internal-services/httpfs/httpfs.py </path/to/data>/http http --lru-capacity 1000 --disk-cache-dir /data/disk-cache --disk-cache-size 4294967296
python /internal-services/httpfs/httpfs.py </path/to/data>/http ftp --lru-capacity 1000 --disk-cache-dir /data/disk-cache --disk-cache-size 4294967296

validate that POSTed viewconfig is indeed a viewconfig

See #10.

At a minimum it should be confirmed that the body of the POST is JSON. But checking the semantics would be even better (although there might be no code to do that on the server ATM).

Delete/organize list entries from HiGlass.io

According to the HiGlass.io documentation, there is an option to use the –project-name parameter with the ingest command. This would allow collapsing by grouping tilesets together as projects.

I got it to work and it's a great step forward!

Yet, there ENORMOUS amount of libraries pulled from HiGlass.io that are unorganized and they clutter up my (large) list of libraries.
I can delete my own entries with list_tilesets / delete_tileset

Is there any way to organize/delete the pulled libraries?

can I omit chr2 parameter?

Hi,

Just curious, in the API doc: https://github.com/higlass/higlass-server/blob/master/API.md

The body needs to contain a BEDPE-like array with the loci determening the fragments to be retrieved. Each locus is represented as an array of the following form:

[ chrom1, start1, end1, chrom2, start2, end2, dataUuid, zoomOutLevel ]

Is it possible to omit chr2, start2 and end2 to get all contacts against chrom1, start1 and end1?

thanks.

request.data.get('datafile') vs request.data['datafile']?

request.data.get('datafile') won't fail immediately if the field is missing, but it will fail just below, at datafile.name. Is there a reason for the get? and it looks like we're expecting either name or datafile, but not both, but one is required?

views.py:

        datafile_name = self.request.data.get('datafile').name

        if 'name' in self.request.data:
            name = self.request.data['name']
        else:
            name = op.split(datafile_name)[1]

app initialisation failing; cannot connect to upstream

We have started getting the following errors in our logs:

2020/01/07 13:56:03 [error] 13#13: *20 connect() failed (111: Connection refused) while connecting to upstream, client: 10.9.0.1, server: , request: "GET /api/v1/viewconfs/?d=default HTTP/1.1", upstream: "uwsgi://127.0.0.1:8001", host: "localhost:8000"

When loading /app there is simply an error message that says:

"Failed to initialize! This is bad, please contact an admin."

We are using higlass-manage (v0.7.3) with mounted tmp and data directories configured to run on port 8000. This issue appears to have started recently but I'm unable to find any other likely cause than an issue with uwsgi.

The process list in the running container looks like this:

UID        PID  PPID  C STIME TTY          TIME CMD
root         1     0  0 13:55 ?        00:00:00 /usr/bin/tini -- supervisord -n
root         6     1  0 13:55 ?        00:00:00 /usr/bin/python /usr/bin/supervisord -n
root         9     6  0 13:55 ?        00:00:00 nginx: master process /usr/sbin/nginx
root        10     6  0 13:55 ?        00:00:00 bash -c mkdir -p /data/log && python manage.py migrate && python manage.py loaddata default-viewconf-fixture.
www-data    13     9  0 13:55 ?        00:00:01 nginx: worker process
www-data    14     9  0 13:55 ?        00:00:01 nginx: worker process
root        28    10  0 13:56 ?        00:00:00 uwsgi --ini /home/higlass/projects/uwsgi.ini --socket :8001 --plugins python --module higlass_server.wsgi --w
root        30    28  0 13:56 ?        00:00:05 uwsgi --ini /home/higlass/projects/uwsgi.ini --socket :8001 --plugins python --module higlass_server.wsgi --w
root        31    28  0 13:56 ?        00:00:07 uwsgi --ini /home/higlass/projects/uwsgi.ini --socket :8001 --plugins python --module higlass_server.wsgi --w
root        32    28  0 13:56 ?        00:00:06 uwsgi --ini /home/higlass/projects/uwsgi.ini --socket :8001 --plugins python --module higlass_server.wsgi --w
root        33    28  1 13:56 ?        00:00:07 uwsgi --ini /home/higlass/projects/uwsgi.ini --socket :8001 --plugins python --module higlass_server.wsgi --w
root       491     0  1 14:07 pts/0    00:00:00 bash
root       507   491  0 14:07 pts/0    00:00:00 ps -ef

–_project-name_ parameter

According to the HiGlass.io documentation, there is an option to use the –project-name parameter with the ingest command. This would allow collapsing by grouping tilesets together as projects.
This would be an amazing feature for me to use with higlass-server/manage.py ingest_tileset, because the amount of libraries I'm adding is very large. Some help in organizing by collapsing would be great.

I pulled higlass to the latest version, but this did not help:
sudo docker pull higlass/higlass-docker
The help function does not display the –project-name parameter:
sudo docker exec gibcus-chicken2.0-higlass python higlass-server/manage.py ingest_tileset -h

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit
  -v {0,1,2,3}, --verbosity {0,1,2,3}
                        Verbosity level; 0=minimal output, 1=normal output,
                        2=verbose output, 3=very verbose output
  --settings SETTINGS   The Python path to a settings module, e.g.
                        "myproject.settings.main". If this isn't provided, the
                        DJANGO_SETTINGS_MODULE environment variable will be
                        used.
  --pythonpath PYTHONPATH
                        A directory to add to the Python path, e.g.
                        "/home/djangoprojects/myproject".
  --traceback           Raise on CommandError exceptions
  --no-color            Don't colorize the command output.
  --filename FILENAME
  --datatype DATATYPE
  --filetype FILETYPE
  --coordSystem COORDSYSTEM
  --coordSystem2 COORDSYSTEM2
  --uid UID
  --name NAME
  --no-upload           Skip upload

Does anyone have advice on organizing my libraries?

SQL injection vulnerability

    query = """
        SELECT importance, chrOffset, fields FROM intervals
        WHERE fields LIKE '%{}%'
        ORDER BY importance DESC
        LIMIT 10
        """.format(text)

    rows = c.execute(query).fetchall()

Maybe something upstream is santitizing text, but still, this is not good. Use the ? instead.

Clean up after test run? / If tests pass, and are immediately rerun, should pass again.

The tests also create an uploads directory in the root higlass-server directory. Can this be placed in /tmp and removed when the tests finished?

Same for db_test.sqlite3.

I am not sure about this. I think we want to be sure tests can be run repeatedly, and if the test fails it can be good to hold on to artifacts from the past run... I guess I don't see cleaning up from a successful run as so important: It's more important to be able to rerun reliably after failed tests.

I might be looking at this the wrong way.

Fresh install fails tests (but just for me?)

Since this morning, tests will not run for me. I've tried fresh installs, but am not getting to the root of it. I had it running under Conda yesterday, but that failed this morning, so I tried running with the default python, hit the same problem. Now I have what I think is an entirely fresh conda install, and am still hitting these issues.

(python2) higlass-server$ which python
/Users/chuck/anaconda3/envs/python2/bin/python
(python2) higlass-server$ python --version
Python 2.7.13 :: Continuum Analytics, Inc.

Other tests also fail, but all the stack traces end the same way:

ERROR: test_get_info (tilesets.tests.GetterTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/chuck/github/hms-dbmi/higlass-server/tilesets/tests.py", line 296, in test_get_info
    info = cch.get_info(filepath)
  File "/Users/chuck/github/hms-dbmi/higlass-server/src/cooler/cooler/contrib/higlass.py", line 163, in get_info
    with h5py.File(file_path, 'r') as f:
  File "/Users/chuck/anaconda3/envs/python2/lib/python2.7/site-packages/h5py/_hl/files.py", line 272, in __init__
    fid = make_fid(name, mode, userblock_size, fapl, swmr=swmr)
  File "/Users/chuck/anaconda3/envs/python2/lib/python2.7/site-packages/h5py/_hl/files.py", line 92, in make_fid
    fid = h5f.open(name, flags, fapl=fapl)
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/Users/travis/build/MacPython/h5py-wheels/h5py/h5py/_objects.c:2687)
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/Users/travis/build/MacPython/h5py-wheels/h5py/h5py/_objects.c:2645)
  File "h5py/h5f.pyx", line 76, in h5py.h5f.open (/Users/travis/build/MacPython/h5py-wheels/h5py/h5py/h5f.c:1933)
IOError: Unable to open file (File signature not found)

/Users/travis is really weird.

Viewconf GET view broken causes 500 error

When requesting http://higlass.io/api/v1/viewconf/ with GET the server throws a 500 error due to:

OperationalError: no such table: tilesets_viewconf

File not deleted when tileset is

When deleting tilesets through the admin interface the related files are not deleted.

Nezar mentioned this causes problems because you end up with files named with uuids without any description. It's hard to clean up afterwards.

Maybe remove files that have been uploaded and renamed by higlass server?

Server doesn't handle tile query errors

When querying for an unknown data set, e.g., http://higlass.io/api/v1/tiles/?d=wurst.3.1, the server returns a 500 error because a DoesNotExist error is not caught.

When querying for a known data set but for a wrong or missing index, e.g., http://higlass.io/api/v1/tiles/?d=CQMd6V_cRw6iCI_-Unl3PQ.4.5, the server returns a 500 error because an IndexError is not caught.

Test files should be removed after testing

Right now a bunch of test files are downloaded (see ./test.sh). There should be a cleaning command or a CLI param to remove files after running the tests.

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