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Hello,
in some cases installation may be performed with a perl intreperter different for the one avaiable on user path. (it is our case).
so in order to use the same perl interpreter it would be nice to change the perl calls to $^X that refers to the running perl used by the scripts.
perl
$^X
as example in autoAugTrain.pl change $cmdString = "grep complete ../pasa/$pasaDBname.assemblies.fasta.transdecoder.cds | perl -pe ".'\'s/>(\S+).*/$1\$/\' | perl -pe \'s#\\.#\\\\.#g\' 1> pasa.complete.lst'; to $cmdString = "grep complete ../pasa/$pasaDBname.assemblies.fasta.transdecoder.cds | $^X -pe ".'\'s/>(\S+).*/$1\$/\' | $^X -pe \'s#\\.#\\\\.#g\' 1> pasa.complete.lst';
autoAugTrain.pl
$cmdString = "grep complete ../pasa/$pasaDBname.assemblies.fasta.transdecoder.cds | perl -pe ".'\'s/>(\S+).*/$1\$/\' | perl -pe \'s#\\.#\\\\.#g\' 1> pasa.complete.lst';
$cmdString = "grep complete ../pasa/$pasaDBname.assemblies.fasta.transdecoder.cds | $^X -pe ".'\'s/>(\S+).*/$1\$/\' | $^X -pe \'s#\\.#\\\\.#g\' 1> pasa.complete.lst';
this could be applied to the following perl scripts.
autoAug.pl autoAugPred.pl autoAugTrain.pl evalCGP.pl eval_dualdecomp.pl eval_multi_gtf.pl hal2maf_split.pl optimize_augustus.pl parseSim4Output.pl peptides2hints.pl runAllSim4.pl writeResultsPage.pl
NB augustify.py and fix_in_frame_stop_codon_genes.py required a manual edition (in our case) in order to set perl interpreter to the correct one.
augustify.py
fix_in_frame_stop_codon_genes.py
regards
Eric
The text was updated successfully, but these errors were encountered:
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Hello,
in some cases installation may be performed with a perl intreperter different for the one avaiable on user path.
(it is our case).
so in order to use the same perl interpreter it would be nice to change the
perlcalls to$^Xthat refers to the running perl used by the scripts.as example in
autoAugTrain.plchange
$cmdString = "grep complete ../pasa/$pasaDBname.assemblies.fasta.transdecoder.cds | perl -pe ".'\'s/>(\S+).*/$1\$/\' | perl -pe \'s#\\.#\\\\.#g\' 1> pasa.complete.lst';to
$cmdString = "grep complete ../pasa/$pasaDBname.assemblies.fasta.transdecoder.cds | $^X -pe ".'\'s/>(\S+).*/$1\$/\' | $^X -pe \'s#\\.#\\\\.#g\' 1> pasa.complete.lst';this could be applied to the following perl scripts.
NB
augustify.pyandfix_in_frame_stop_codon_genes.pyrequired a manual edition (in our case) in order to setperlinterpreter to the correct one.regards
Eric
The text was updated successfully, but these errors were encountered: