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loosolab / TOBIAS_snakemake

Snakemake pipeline for running TOBIAS analysis
MIT License
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Dependency is missing in rule join_bound #9

Closed aksarkar closed 1 year ago

aksarkar commented 1 year ago

I am running the pipeline using --use-conda; however, the environment used for the rule join_bound in footprinting.snake does not appear to have the required dependency

/bin/bash: igvtools: command not found
[elided]
RuleException:
CalledProcessError in file /mnt/fsx/scratch/asarkar/TOBIAS_snakemake/snakefiles/footprinting.snake, line 157:
Command 'set -euo pipefail;  igvtools index bmmc-topic-4-gmm-3-cluster-0/overview/all_6h_control_bound.bed' returned non-zero exit status 127.
  File "/mnt/fsx/scratch/asarkar/TOBIAS_snakemake/snakefiles/footprinting.snake", line 157, in __rule_join_bound
  File "/home/ec2-user/mambaforge3/envs/bap/lib/python3.9/concurrent/futures/thread.py", line 58, in run
Removing output files of failed job join_bound since they might be corrupted:
[elided]
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2023-06-08T181331.925143.snakemake.log
msbentsen commented 1 year ago

Hi @aksarkar,

The dependency is available in the upper snakemake environment (the one used when starting the snakemake), as seen here: https://github.com/loosolab/TOBIAS_snakemake/blob/842b6c897d6bdb33e574199367c4d54e8c9e9592/environments/snakemake.yaml#L10-L12

If you install this environment first, it will be available for the rule:

$ conda env create -f environments/snakemake.yaml
$ conda activate tobias_snakemake_env

Or you might install igvtools in your current environment. Hope that answers the question.