PhyloSkims/annotate
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Patch a bug to launch exonerate on complexe filename

Browse Source 
Former-commit-id: fd381611fc7ec543f374e8c6132d29c66612f1a4
Former-commit-id: 653603e547c675c80ace6a3a9d0f13be89048017
This commit is contained in:
Eric Coissac
2018-01-24 14:30:00 +01:00
parent 4c7ba137d9
commit 2e5bdf2246
2 changed files with 18 additions and 1 deletions
Download Patch File Download Diff File Expand all files Collapse all files

15
detectors/cds/bin/do_exonerate.csh
View File

@ -110,8 +110,21 @@ set base = $OutDir/$GenoName.$ProtName
# #
# Alias the genome filename to a short name # Alias the genome filename to a short name
# to circumvent a bug in exonerate # to circumvent a bug in exonerate
echo $GenoFile | grep '^/' > /dev/null
if ( $status == 1 ) then
set AbsGenoFile = `pwd`/$GenoFile
set DirGenoFile = `dirname $AbsGenoFile`
set DirGenoFile = `(cd $DirGenoFile;pwd)`
set AbsGenoFile = $DirGenoFile/`basename $AbsGenoFile`
else
set AbsGenoFile = $GenoFile
endif
set ShortLink = $OutDir/genome.fasta set ShortLink = $OutDir/genome.fasta
ln -s $GenoFile $ShortLink ln -s $AbsGenoFile $ShortLink
Notify " Building input shortcut $AbsGenoFile --> $ShortLink"
ls -l $ShortLink
# #
# skip exonerate calculations if already done # skip exonerate calculations if already done

4
detectors/cds/bin/go_cds.csh
View File

@ -63,6 +63,8 @@ foreach dir ("core" "shell" "dust")
endif endif
end end
cp $temp/ $Genome.cds.fasta $Genome.cds.fasta
# #
# pass2: transsplicing # pass2: transsplicing
# #
@ -71,6 +73,8 @@ end
# pass3: prokov # pass3: prokov
# #
$PROG_DIR/do_prokov.sh $Fasta $Genome.cds.fasta $temp
# #
# end : output on stdout # end : output on stdout
# #