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CCBR / RENEE

A comprehensive quality-control and quantification RNA-seq pipeline
https://CCBR.github.io/RENEE/
MIT License
3 stars 4 forks source link

snakemake/singularity loading error on main branch of 2.5.11-dev #121

Closed slsevilla closed 5 months ago

slsevilla commented 6 months ago

I pulled a clone for RENEE and am on the main branch. I tried to deploy the pipeline and ran into this error

[+] Loading singularity  4.0.1  on cn4305 
RENEE (v2.5.11-dev)
Are singularity and snakemake in your PATH? Please check before proceeding again!
Command '['snakemake', '-npr', '-s', 'workflow/Snakefile', '--use-singularity', '--rerun-incomplete', '--cores', '4', '--configfile=config.json']' returned non-zero exit status 1.
Config file config.json is extended by additional config specified via the command line.
SyntaxError in file /vf/users/CCBR/projects/ccbr1327_ssc/ssc_20240326/workflow/rules/common.smk, line 266:
Command must be given as string after the shell keyword. (common.smk, line 266)
  File "/vf/users/CCBR/projects/ccbr1327_ssc/ssc_20240326/workflow/Snakefile", line 218, in <module>

Unsure why this is happening, but it is also no longer loading snakemake or singularity in my path.

kelly-sovacool commented 6 months ago

this happens when you call bin/renee?

slsevilla commented 6 months ago

Yes, command:

/data/CCBR_Pipeliner/Pipelines/RENEE/renee-dev-sevillas2/bin/renee run \
    --input  /vf/users/CCBR/rawdata/ccbr1327/psomagen_delivery/fastq_files/* \
    --genome mm10_M25 \
    --mode slurm \
    --output /data/CCBR/projects/ccbr1327_ssc/ssc_20240326 \
    --sif-cache /data/CCBR_Pipeliner/SIFS
kelly-sovacool commented 5 months ago

I was not able to reproduce this error with the test dataset