Snakemake_ATAC_2020 issueshttps://git.lumc.nl/jchouaref/Snakemake_ATAC_2020/-/issues2021-03-19T11:36:25+01:00https://git.lumc.nl/jchouaref/Snakemake_ATAC_2020/-/issues/11Pipeline not working on dev branch2021-03-19T11:36:25+01:00ChouarefPipeline not working on dev branch*Created by: JihedC*
Hi Jianhui,
I was trying to run the pipeline on shark but I have got this error message:
'''
Start time : Wed Mar 17 14:35:21 CET 2021
/exports/humgen/jihed/miniconda3/lib/python3.6/site-packages/snakemake/wor...*Created by: JihedC*
Hi Jianhui,
I was trying to run the pipeline on shark but I have got this error message:
'''
Start time : Wed Mar 17 14:35:21 CET 2021
/exports/humgen/jihed/miniconda3/lib/python3.6/site-packages/snakemake/workflow.py:26: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'.
from snakemake.parser import parse
Building DAG of jobs...
Creating conda environment envs/homer.yaml...
Downloading remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /exports/humgen/jihed/Jianhui/Snakemake_ATAC_2020/ATAC-seq_pipeline/rules/../envs/homer.yaml:
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
ResolvePackageNotFound:
- hmmratac=4.11
End time : Wed Mar 17 14:35:39 CET 2021
'''
I think there is a mistake with the version of hmmratac. On conda I can find only hmmratac 1.2.10.
Can you fix this please?https://git.lumc.nl/jchouaref/Snakemake_ATAC_2020/-/issues/8HMMRATAC is not downloaded by the pipeline2021-01-04T17:28:30+01:00ChouarefHMMRATAC is not downloaded by the pipeline*Created by: JihedC*
Now HMMRATAC works but the tool is not downloaded by the pipeline.
We can either add a rule to download it from GitHub (also include a touch command) or try to use the conda version of HMMRATAC.
First try conda...*Created by: JihedC*
Now HMMRATAC works but the tool is not downloaded by the pipeline.
We can either add a rule to download it from GitHub (also include a touch command) or try to use the conda version of HMMRATAC.
First try conda, it's the simplest.https://git.lumc.nl/jchouaref/Snakemake_ATAC_2020/-/issues/4Coverage over other bed files2020-12-28T12:11:30+01:00ChouarefCoverage over other bed files*Created by: JihedC*
For now the pipeline uses the gencode bedfile to measure chromatin accessibility around the gene body.
We want to include other bedfiles, such as protein binding sites or repeat.
*Created by: JihedC*
For now the pipeline uses the gencode bedfile to measure chromatin accessibility around the gene body.
We want to include other bedfiles, such as protein binding sites or repeat.