Error when running skipper in paired end mode

[Aravind-sunda]

skipper/rules/basic/pe_preprocess.smk

Line 136 in 7fa1392

tmpdir = "/tscc/nfs/home/hsher/scratch/singularity_tmp",

When running Skipper in paired-end (PE) mode, Snakemake fails during job preparation with a permission error because the workflow tries to create/use a TSCC-specific temp path under /tscc. This appears to be caused by a hard-coded tmpdir value in skipper/rules/basic/pe_preprocess.smk.

[augustboyle]

Perhaps the directory could be easily updated for general use, but another option is to use the publication release of the software, which has a lot of flexibility for providing dependencies and paths: https://github.com/YeoLab/skipper/releases/tag/v1.1.0
You will have to be more mindful about using the software run at the time.