Hi
I updated the packaging of optimir in Git[1] but its autopkgtest
fails with
autopkgtest [22:45:20]: test run-sample-analysis: [-----------------------
#########################
## OPTIMIR ##
#########################
Starting workflow for sample S1
> Starting Library preparation...
Error with system call: Bowtie2 index creation failed: command line =
bowtie2-build -f
/tmp/autopkgtest.FxuHx2/autopkgtest_tmp/OptimiR_Results_Dir/OptimiR_lib/fasta/optimiR_library.fa
/tmp/autopkgtest.FxuHx2/autopkgtest_tmp/OptimiR_Results_Dir/OptimiR_lib/bowtie2_index/optimiR_alignment_library
-q
Check that path to Bowtie2, Cutadapt, Samtools are well defined.
autopkgtest [22:45:21]: test run-sample-analysis: -----------------------]
autopkgtest [22:45:21]: test run-sample-analysis: - - - - - - - - - - results
- - - - - - - - - -
I have not spent much time into investigating this issue - may be
somebody might beat me in this.
Kind regards
Andreas.
[1] https://salsa.debian.org/med-team/optimir
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