Comments (21)
katsikora
commented on September 3, 2024
1
ah sorry, it should perhaps read git clone instead of git checkout
from snakepipes.
sunta3iouxos
commented on September 3, 2024
1
In addition, shouldn't I first activate the snakepipes_develop and then do pip install --upgrade . ? because where pip will do the update? I assume in the base environment
from snakepipes.
katsikora
commented on September 3, 2024
Hi,
I see where this error from Genrich peak calling rule would arise if you don't have input samples as control. This is an unintended bug and can be fixed. Genrich should be able to call peaks even if input control is missing.
Best wishes,
Katarzyna
from snakepipes.
sunta3iouxos
commented on September 3, 2024
Also , Genrich provides qvalues in the manner of the IDR approach by taking into account the biological replicates. Is it possible to also add this? the replicates can also be taken from the sample sheet.
from snakepipes.
katsikora
commented on September 3, 2024
Also , Genrich provides qvalues in the manner of the IDR approach by taking into account the biological replicates. Is it possible to also add this? the replicates can also be taken from the sample sheet.
This we already have implemented.
from snakepipes.
sunta3iouxos
commented on September 3, 2024
This we already have implemented.
So it did not work for me due to the lack of input. Could you please direct me to the relevant information so that I could properly use this option?
Thank you
from snakepipes.
katsikora
commented on September 3, 2024
I've pushed a fix to the develop branch. Do you want to try to install the development snakePipes version and try it out?
It should work without input now, as expected for cutN'x experiments.
from snakepipes.
sunta3iouxos
commented on September 3, 2024
I've pushed a fix to the develop branch. Do you want to try to install the development snakePipes version and try it out? It should work without input now, as expected for cutN'x experiments.
I would like to, unfortunately I have installed snakePipes via conda. Is there a way to update the pipeline to the development version using conda/mamba?
If else, is there a way to manually do this?
Thank you!
from snakepipes.
katsikora
commented on September 3, 2024
git checkout -b develop https://github.com/maxplanck-ie/snakepipes.git snakepipes_develop_folder
conda env create -n snakepipes_develop
mamba install -n snakepipes_develop pip
cd snakepipes_develop_folder
pip install --upgrade .
snakepipes config (with your standard options)
Then you should be good to go to conda activate snakepipes_develop and run the workflows.
Best,
Katarzyna
from snakepipes.
sunta3iouxos
commented on September 3, 2024
got an issue:
git checkout -b develop https://github.com/maxplanck-ie/snakepipes.git snakepipes_develop_folder
fatal: not a git repository (or any of the parent directories): .gitI assume that I can download directly the folder via github
from snakepipes.
sunta3iouxos
commented on September 3, 2024
unfortunately I got an error:
Building wheel for datrie (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for datrie (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [74 lines of output]and then:
error: command '/usr/bin/gcc' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for datrie
Building wheel for stopit (setup.py) ... done
Created wheel for stopit: filename=stopit-1.1.2-py3-none-any.whl size=11939 sha256=6ef399146fe9c7647d6f6f00f4dde98429a83ec5bccc33ff98ba820909be2d6d
Stored in directory: /home/tgeorgom/.cache/pip/wheels/10/10/63/c3c98c9859d2aa59553536cc2ea005d3c9c39e214ab4fd614c
Successfully built snakePipes connection-pool stopit
Failed to build datrie
ERROR: Could not build wheels for datrie, which is required to install pyproject.toml-based projectsfrom snakepipes.
katsikora
commented on September 3, 2024
Alright, thanks for reporting that one, I've seen it before. It's related to some dependency builds failing for python 3.12.
I'll have to cap the python version until this is fixed.
For now, you can run
conda env create -n snakepipes_develop python=3.11
or mamba install -n snakepipes_develop python=3.11
before running pip install
from snakepipes.
katsikora
commented on September 3, 2024
In addition, shouldn't I first activate the snakepipes_develop and then do
pip install --upgrade .? because where pip will do the update? I assume in the base environment
That's right, it's better if you conda activate snakepipes_develop first.
from snakepipes.
sunta3iouxos
commented on September 3, 2024
snakepipes config (with your standard options)
How am I transferring my settings to the new development environment? Or how am I linking the old settings to the newer one?
Thank you!
from snakepipes.
sunta3iouxos
commented on September 3, 2024
I've run into some errors.
What I did.
git clone -b develop https://github.com/maxplanck-ie/snakepipes.git snakepipes_develop_folder
cd snakepipes_develop_folder/
mamba create -n snakePipes_devel python=3.11 pip
mamba activate snakePipes_devel
cd ../snakepipes_develop_folder
pip install --upgrade .Then I copied some files from my stable environment:
cp -r /scratch/tgeorgom/mamba/snakePipes/lib/python3.11/site-packages/snakePipes/shared/* /scratch/tgeorgom/mamba/snakePipes_devel/lib/python3.11/site-packages/snakePipes/shared/
cp /scratch/tgeorgom/mamba/snakePipes/lib/python3.11/site-packages/snakePipes/shared/organisms/* /scratch/tgeorgom/mamba/snakePipes_devel/lib/python3.11/site-packages/snakePipes/shared/organisms/
cp -r /scratch/tgeorgom/mamba/snakePipes/lib/python3.11/site-packages/snakePipes/workflows/* /scratch/tgeorgom/mamba/snakePipes_devel/lib/python3.11/site-packages/snakePipes/workflows/first config:
snakePipes config gives the correct parameters
--- Final Updated Config ---------------------------------------------------------------------
config file: /scratch/tgeorgom/mamba/snakePipes_devel/lib/python3.11/site-packages/snakePipes/shared/defaults.yaml
clusterConfig: shared/cluster.yaml
condaEnvDir: None
configMode: manual
emailSender: None
max_thread: 4
oldConfig: None
onlySSL: False
organismsDir: shared/organisms
smtpPassword: None
smtpPort: 0
smtpServer: None
smtpUsername: None
snakemakeOptions: --use-conda --conda-prefix /scratch/tgeorgom/mamba/snakePipes/envs
tempDir: /scratch/tgeorgom/temp/
toolsVersion: True
--------------------------------------------------------------------------------The createEnvs returns an error:
snakePipes createEnvs
Traceback (most recent call last):
File "/scratch/tgeorgom/mamba/snakePipes_devel/bin/snakePipes", line 441, in <module>
main(sys.argv[1:])
File "/scratch/tgeorgom/mamba/snakePipes_devel/bin/snakePipes", line 435, in main
createCondaEnvs(args)
File "/scratch/tgeorgom/mamba/snakePipes_devel/bin/snakePipes", line 322, in createCondaEnvs
md5hash.update(condaDirUse.encode())
^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'encode'from snakepipes.
katsikora
commented on September 3, 2024
Hi,
indeed the behaviour of snakePipes config and snakePipes createEnvs has changed such that snakePipes config now accepts the argument --condaEnvDir, in which snakePipes createEnvs is going to create the environments. Also snakemakeOptions --use-conda --conda-prefix are removed from the config and hard-coded in the snakemake command.
Briefly, running snakePipes config --condaEnvDir /scratch/tgeorgom/mamba/snakePipes/envs and then snakePipes createEnvs should be sufficient to be able to run the workflows.
Best wishes,
Katarzyna
from snakepipes.
NixBio
commented on September 3, 2024
Thank you for your message. I am out of office. I will answer your email once I am back in my office.
In urgent cases, please, contact genomics-core(at)rcii.de
Kind Regards,
Nicholas Strieder
--
Dr. rer. nat. Nicholas Strieder
~~
Leibniz-Institut für Immuntherapie - LIT
NGS Core - Bininformatics
Universitätsklinikum Regensburg
Franz-Josef-Strauß-Allee 11
93053 Regensburg
Germany
Phone: ++49 (0)941 944 18188
E-mail: ***@***.***
>> Katarzyna Sikora ***@***.***> 2.11.23 13:07 >>>
Hi,
indeed the behaviour of `snakePipes config` and `snakePipes createEnvs` has changed such that `snakePipes config` now accepts the argument `--condaEnvDir`, in which it is going to create the environments. `snakePipes createEnvs` would use this path then. Also `snakemakeOptions --use-conda --conda-prefix` are removed from the config and hard-coded in the snakemake command.
Briefly, running `snakePipes config --condaEnvDir /scratch/tgeorgom/mamba/snakePipes/envs` and then `snakePipes createEnvs` should be sufficient to be able to run the workflows.
Best wishes,
Katarzyna
…--
Reply to this email directly or view it on GitHub:
#945 (comment)
You are receiving this because you are subscribed to this thread.
Message ID: ***@***.***>
from snakepipes.
sunta3iouxos
commented on September 3, 2024
The initiation worked but when I started the analysis I got the following error:
---- This analysis has been done using snakePipes version 2.7.3 ----
Sample sheet found and header is ok!
Building DAG of jobs...
InputFunctionException in line 164 of /scratch/tgeorgom/mamba/snakePipes_devel/lib/python3.11/site-packages/snakePipes/shared/rules/ChIP_peak_calling_spikein.snakefile:
Error:
TypeError: can only concatenate str (not "bool") to str
Wildcards:
group=DMSO_POLII
Traceback:
File "/scratch/tgeorgom/mamba/snakePipes_devel/lib/python3.11/site-packages/snakePipes/shared/rules/ChIP_peak_calling_spikein.snakefile", line 167, in <lambda>
File "/scratch/tgeorgom/mamba/snakePipes_devel/lib/python3.11/site-packages/snakePipes/shared/rules/ChIP_peak_calling_spikein.snakefile", line 167, in <listcomp>
Spikein genome detected - at least one spikeIn chromosome found with extention _spikein .
The command I used is:
ChIP-seq -d /scratch/tgeorgom/AP04/ --useSpikeInForNorm --getSizeFactorsFrom genome --peakCaller Genrich --peakCallerOptions "-y -a 1 -e chrM,chrY -q 0.01" --sampleSheet /scratch/tgeorgom/AP04/PolII.tsv --windowSize 500 --plotFormat "pdf" mm10_gencodeM19_spikesTEST /scratch/tgeorgom/AP04/PolII_ChIPtype_all.yalmfrom snakepipes.
katsikora
commented on September 3, 2024
Hmm, this looks like the error you originally reported.
from snakepipes.
katsikora
commented on September 3, 2024
cp -r /scratch/tgeorgom/mamba/snakePipes/lib/python3.11/site-packages/snakePipes/shared/* /scratch/tgeorgom/mamba/snakePipes_devel/lib/python3.11/site-packages/snakePipes/shared/
I think this might have overwritten the changes I made to the Genrich rule in the develop branch.
from snakepipes.
katsikora
commented on September 3, 2024
The fix is now part of snakePipes 2.8.0, 2.8.1.
from snakepipes.
Related Issues (20)
- add allelic-counting mode to mRNA seq
- fix SEACR with control
- error in ChIP-seq HOT 2
- update the snakePipes installed from the github
- Error in mRNA-seq allelic-mapping when using custom genome
- mRNA-seq: sambamba markdup fails because "too many open files"
- plotFinger fails due to insaficient wall time HOT 6
- [Question] where to find the exact command issued? HOT 2
- [Request] looping inputs for multiple ChIP-seq comparisons HOT 1
- allow user to specify mincount for filtering windows for DB with CSAW
- snakePipes createEnvs fails HOT 1
- add support for custom model formula to mRNAseq and other workflows HOT 2
- DNA-mapping allelic mode - NMaskindex / SNPfile combination
- error in createIndices: module 'pulp' has no attribute 'list_solvers'. Did you mean: 'listSolvers'? HOT 3
- snakePipes envInfo: AttributeError: 'NoneType' object has no attribute 'encode' HOT 4
- conda and "strict channel priorities" HOT 2
- allow for custom bed to be used as input to CSAW for DB
- fix nearest Gene annotation on CSAW_DBR
- Genrich -e option addition
- add peak qc for SEACR as for MACS2 HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
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.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from snakepipes.