Absence of NOVOSORT makes to IRFinder v1.3.1 exit with code 1 but no error message

williamritchie / IRFinder

Detecting intron retention from RNA-Seq experiments

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Absence of NOVOSORT makes to IRFinder v1.3.1 exit with code 1 but no error message #109

Closed tbrittoborges closed 4 years ago

tbrittoborges commented 4 years ago

Dear Dadi,

The new (DOSORT option)[https://github.com/williamritchie/IRFinder/blob/bc350669b60d3b7b22e19abf5c732b3bdcb9d3a9/bin/IRFinder#L104] makes IRFinder -m BAM exit with code 1 if NOVOSORT tool is not present. NOVOSORT is not in the requirements. Manually setting DOSORT=0 fixes the issue.

All the best, Thiago

Versions:

	version
bedtools	2.29.2
conda	4.8.4
glib	2.65.0
pysam	0.15.3
samtools	1.7
star	2.7.5b
irfinder	1.3.1

dg520 commented 4 years ago

Hi @tbrittoborges ,

Thank you for reporting this. You're right. Adding set -e to the wrapper makes IRFinder quit if no Novosort installed on the machine.
I've now commented out the set -e part, as we still want to keep sorting as the default and -u for not sorting as an option. This literally flips it back to the previous version of wrapper that works. The new codes have been merged.

Best,
Dadi