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KoesGroup / Snakemake_ChIPseq_PE

Pipeline for the analysis of PE ChIP-seq data
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Merge bed branch to develop branch #7

Closed JihedC closed 6 years ago

JihedC commented 6 years ago

Hi all, I would like to merge the bed branch to the develop branch. The rules for peak calling seems to work. Could you try on your own side?

There is still a lot of changes and optimisation to do, especially on the method used to defined treatment and control samples. But it can be done on the develop branch I think.

Cheers, Jihed

JihedC commented 6 years ago

I should update the README, they are many more outputs now :P

mgalland commented 6 years ago

Hello Jihed. In the future, when you ask for tests, maybe it would be wise to specify how snakemake should be run. For instance, if one needs to run snakemake --use-conda or simply snakemake but then after activating the environment. That's probably why specifying the --use-conda is handy in the future (no need to install and activate an environment). For now, it's ok, I know my way!

JihedC commented 6 years ago

Ok!

mgalland commented 6 years ago

For now, I find this mistake:

CondaEnvironmentNotFoundError: Could not find environment: macs2 .
You can list all discoverable environments with `conda info --envs`.

    Error in rule call_narrow_peaks:
        jobid: 13
        output: results/bed/ChIP1_vs_ChIP2_L1_peaks.narrowPeak

RuleException:
CalledProcessError in line 267 of /home/mgalland/workspace/DMC1_ChIPseq/Snakefile:
Command ' set -euo pipefail;  
        source activate macs2
        macs2 callpeak -t results/mapped/ChIP1_L1.sorted.rmdup.bam -c results/mapped/ChIP2_L1.sorted.rmdup.bam --format BAMPE --gsize mm --name ChIP1_vs_ChIP2_L1 --nomodel --bdg -q 0.05 --outdir results/bed/ ' returned non-zero exit status 1.
  File "/home/mgalland/workspace/DMC1_ChIPseq/Snakefile", line 267, in __rule_call_narrow_peaks
  File "/home/mgalland/workspace/scripts/miniconda3/envs/DMC1/lib/python3.6/concurrent/futures/thread.py", line 56, in run

This has to do with the source activate macs2 line. This line is not needed if you run snakemake with the snakemake --use-conda command provided that you dispose of a envs/mac2_env.yaml file.

JihedC commented 6 years ago

Make sense, it's only on my computer that I named the environment for macs2 : 'macs2'. I'll change that. You didn't get an error with another rule?

mgalland commented 6 years ago

Only this mistake. I have a hard time working on issue #8 because this issue is in the way. Instead of merging the bed branch to the develop branch, I think we need to fix issues #7 and #8

JihedC commented 6 years ago

I have tested the branch on my local computer and everything seems to work fine, I think the issues #8 #10 are solved on this branch. I still have to control for the #9