Run fasta_header_fix.pl on fasta files before submitting to queue

svn path=/; revision=43

diff --git a/server_admin_scripts/run_inparanoid.sh b/server_admin_scripts/run_inparanoid.sh
index 5b0a014027c12c51538e3784d8a56a258f12784a..afe3fd9439390c5c11e154b7794f9210d5e27665 100755 (executable)
--- 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