102258 2005-08-12 09:12 0000 sci-biology/trnascan-se-1.23 is broken#: 1) missing soft links 2) wrong hard-coded paths 2005-08-12 14:18:27 0000 1 1 1 Unclassified Gentoo Linux Applications unspecified x86 Linux RESOLVED FIXED P2 critical --- 1 tlombard@mpi-bremen.de ribosome@gentoo.org sci@gentoo.org tlombard@mpi-bremen.de 2005-08-12 09:12:48 0000 # 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 ribosome@gentoo.org 2005-08-12 14:18:27 0000 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.