# The gentoo ebuild sci-biology/trnascan-se-1.23 is broken
# 1) missing soft links
# 2) wrong hard-coded path in the main perl script
#
###################
# fix soft links:
ln -s /usr/share/trnascan-se/TPCsignal /usr/bin/TPCsignal
ln -s /usr/share/trnascan-se/Dsignal /usr/bin/Dsignal
###################
# fix paths in file tRNAscan-SE (main perl sript of tRNA-scan-SE)
rhone bin # diff tRNAscan-SE.orig tRNAscan-SE
647c647
< $lib_dir =
"/var/tmp/portage/trnascan-se-1.23/image//usr/share/trnascan-se/";
---
> $lib_dir = "/usr/share/trnascan-se/";
649c649
< $bindir ="/var/tmp/portage/trnascan-se-1.23/image//usr/bin/";
# modified by 'make'
---
> $bindir ="/usr/bin/"; # modified by 'make'
1441,1442c1441,1442
< elsif (-r
"/var/tmp/portage/trnascan-se-1.23/image//usr/share/trnascan-se/".$gc_file)
{
< $gc_file_path =
"/var/tmp/portage/trnascan-se-1.23/image//usr/share/trnascan-se/".$gc_file;
---
> elsif (-r "/usr/share/trnascan-se/".$gc_file) {
> $gc_file_path = "/usr/share/trnascan-se/".$gc_file;
Reproducible: Always
Steps to Reproduce:
1. emerge sci-biology/trnascan-se-1.23
2. run a test analysis e.g. "./tRNAscan-SE.orig /tmp/test.fasta" , where
test.fasta is a dna sequence file in FASTA format
Actual Results:
FATAL: Unable to open TRNA2-euk.cm covariance model file
Expected Results:
write results to standard output
Thanks for reporting, Thierry. I fixed the problem. (Symlinks were not
necessary once the hard-coded paths were corrected; all files were found
without problem and I successfully tested some random DNA sequence for
tRNA presence.)
Merci, et bonne chance dans tes travaux.
