Bug 102258 – sci-biology/trnascan-se-1.23 is broken#: 1) missing soft links 2) wrong hard-coded paths

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Thierry Lombardot 2005-08-12 09:12:48 UTC]

# 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

[Comment 1 Olivier Fisette (RETIRED) 2005-08-12 14:18:27 UTC]

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.