Giter Club home page Giter Club logo

Comments (7)

AndreaGuarracino avatar AndreaGuarracino commented on August 11, 2024 1

I am working on this bioconda/bioconda-recipes#38875

from pggb.

subwaystation avatar subwaystation commented on August 11, 2024

After a manual copy I get

(pggb) [heumos@savasana ~]$ partition-before-pggb -i ~/git/pggb/data/HLA/DRB1-3123.fa.gz -o test_partition -n 12 -t 16 -p 70 
[wfmash::map] Reference = [/home/heumos/git/pggb/data/HLA/DRB1-3123.fa.gz]
[wfmash::map] Query = [/home/heumos/git/pggb/data/HLA/DRB1-3123.fa.gz]
[wfmash::map] Kmer size = 19
[wfmash::map] Window size = 30
[wfmash::map] Segment length = 5000 (read split allowed)
[wfmash::map] Block length min = 25000
[wfmash::map] Chaining gap max = 100000
[wfmash::map] Percentage identity threshold = 70%
[wfmash::map] Skip self mappings
[wfmash::map] Mapping output file = /dev/stdout
[wfmash::map] Filter mode = 1 (1 = map, 2 = one-to-one, 3 = none)
[wfmash::map] Execution threads  = 16
[wfmash::skch::Sketch::build] minimizers picked from reference = 10970
[wfmash::skch::Sketch::index] unique minimizers = 2797
[wfmash::skch::Sketch::computeFreqHist] Frequency histogram of minimizers = (1, 19) ... (22, 1)
[wfmash::skch::Sketch::computeFreqHist] With threshold 0.001%, consider all minimizers during lookup.
[wfmash::map] time spent computing the reference index: 0.015768 sec
[wfmash::skch::Map::mapQuery] mapped 100.00% @ 3.25e+05 bp/s elapsed: 00:00:00:00 remain: 00:00:00:00
[wfmash::skch::Map::mapQuery] count of mapped reads = 11, reads qualified for mapping = 12, total input reads = 12, total input bp = 163416
[wfmash::map] time spent mapping the query: 5.04e-01 sec
[wfmash::map] mapping results saved in: /dev/stdout
wfmash -s 5000 -l 25000 -p 70 -n 11 -k 19 -H 0.001 -X -t 16 --tmp-base test_partition /home/heumos/git/pggb/data/HLA/DRB1-3123.fa.gz --approx-map
0.39s user 2.04s system 461% cpu 0.52s total 69280Kb max memory
python3 /home/heumos/miniconda3/envs/pggb/bin/scripts/paf2net.py -p test_partition/DRB1-3123.fa.gz.6deb21e.mappings.wfmash.paf
0.02s user 0.00s system 95% cpu 0.02s total 10044Kb max memory
Traceback (most recent call last):
  File "/home/heumos/miniconda3/envs/pggb/bin/scripts/net2communities.py", line 19, in <module>
    import igraph as ig
ModuleNotFoundError: No module named 'igraph'
Command exited with non-zero status 1
python3 /home/heumos/miniconda3/envs/pggb/bin/scripts/net2communities.py -e test_partition/DRB1-3123.fa.gz.6deb21e.mappings.wfmash.paf.edges.list.txt -w test_partition/DRB1-3123.fa.gz.6deb21e.mappings.wfmash.paf.edges.weights.txt -n test_partition/DRB1-3123.fa.gz.6deb21e.mappings.wfmash.paf.vertices.id2name.txt --accurate-detection --output-prefix test_partition/DRB1-3123.fa.gz.6deb21e
0.01s user 0.00s system 95% cpu 0.02s total 10164Kb max memory

from pggb.

AndreaGuarracino avatar AndreaGuarracino commented on August 11, 2024

Dependencies, dependencies everywhere.

What did you do exactly with the 'manual copy'?

from pggb.

subwaystation avatar subwaystation commented on August 11, 2024
mkdir /home/heumos/miniconda3/envs/pggb/bin/scripts
cp ~/git/pggb/scripts/* /home/heumos/miniconda3/envs/pggb/bin/scripts/

from pggb.

subwaystation avatar subwaystation commented on August 11, 2024

I did a new installation bioconda/bioconda-recipes#38875, but the scripts directory is still missing essential scripts:

ls /home/heumos/miniconda3/envs/pggb/bin/scripts
nucmer2vcf.R  vcf_preprocess.sh

To confirm I installed the correct conda package I did:

igraph
No configuration file, using defaults
igraph 0.10.3 running inside Python 3.10.8 | packaged by conda-forge | (main, Nov 22 2022, 08:23:14) [GCC 10.4.0] on linux

from pggb.

subwaystation avatar subwaystation commented on August 11, 2024

What you currently have:

mv pggb $PREFIX/bin
mv partition-before-pggb $PREFIX/bin
mv scripts/*.py $PREFIX/bin
mv scripts $PREFIX/bin

Since you already moved the Python scripts, they won't be in the scripts folder anymore. So I would suggest:

mv pggb $PREFIX/bin
mv partition-before-pggb $PREFIX/bin
cp scripts/*.py $PREFIX/bin
mv scripts $PREFIX/bin

Also please add a tiny test so we can detect such errors while packaging.

from pggb.

subwaystation avatar subwaystation commented on August 11, 2024

Finally, it works :)

from pggb.

Related Issues (20)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.