From 148ef0b7d630174c0c2e7059733cadd82cbf36a8 Mon Sep 17 00:00:00 2001 From: elserj Date: Tue, 21 Sep 2010 23:17:18 +0000 Subject: [PATCH] Run fasta_header_fix.pl on fasta files before submitting to queue svn path=/; revision=43 --- server_admin_scripts/run_inparanoid.sh | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/server_admin_scripts/run_inparanoid.sh b/server_admin_scripts/run_inparanoid.sh index 5b0a014..afe3fd9 100755 --- a/server_admin_scripts/run_inparanoid.sh +++ b/server_admin_scripts/run_inparanoid.sh @@ -11,17 +11,19 @@ do dirname=${lsarray[$i]}_______${lsarray[$j]} echo $dirname mkdir $dirname - cp ${lsarray[$i]} ${lsarray[$j]} $dirname + #cp ${lsarray[$i]} ${lsarray[$j]} $dirname + fasta_header_fix.pl ${lsarray[$i]} $dirname/${lsarray[$i]} + fasta_header_fix.pl ${lsarray[$j]} $dirname/${lsarray[$j]} cd $dirname - cp ../../inparanoid.pl ./ - cp ../../blast_parser.pl ./ - cp ../../BLOSUM62 ./ - cp ../../InparanoidXMLCreator.pl ./ - cp ../../seqstat.jar ./ + cp /home/bpp/elserj/Orthology_software/inparanoid/inparanoid.pl ./ + cp /home/bpp/elserj/Orthology_software/inparanoid/blast_parser.pl ./ + cp /home/bpp/elserj/Orthology_software/inparanoid/BLOSUM62 ./ + cp /home/bpp/elserj/Orthology_software/inparanoid/InparanoidXMLCreator.pl ./ + cp /home/bpp/elserj/Orthology_software/inparanoid/seqstat.jar ./ echo '#!/bin/bash #$ -cwd /usr/bin/perl inparanoid.pl '${lsarray[$i]} ${lsarray[$j]}'' > inparanoid_sub -# qsub inparanoid_sub + qsub inparanoid_sub cd .. done done -- 2.34.1