From a83a510468c1c4346e262158e7219c97be25513d Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Mon, 12 Aug 2013 15:19:41 +0100
Subject: [PATCH] fix for bash

---
 lib/j2ssh/j2ssh.properties | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/lib/j2ssh/j2ssh.properties b/lib/j2ssh/j2ssh.properties
index eeb9581e0..ee97c8a7f 100644
--- a/lib/j2ssh/j2ssh.properties
+++ b/lib/j2ssh/j2ssh.properties
@@ -11,15 +11,12 @@ host=localhost
 #
 # Sanger options
 # 
-#bsub=bsub -q normal -n 1 -R 'select[blast && mem > 500] rusage[mem=500]' 
-bsub=bsub -q normal -n 1 -R 'select[mem > 500] rusage[mem=500]' 
+bsub=source .profile; bsub -q normal -n 1 -R 'select[mem > 500] rusage[mem=500]' 
 blastp=-I /software/pathogen/psu_svn/trunk/genexec/perl/src/flexi_blast.pl -p 
 blastx=-I /software/pathogen/psu_svn/trunk/genexec/perl/src/flexi_blast.pl -x
 tblastx=-I /software/pathogen/psu_svn/trunk/genexec/perl/src/flexi_blast.pl -tx
 blastn=-I /software/pathogen/psu_svn/trunk/genexec/perl/src/flexi_blast.pl
 
-#fasta=-I /nfs/disk222/yeastpub/bio-soft/fasta/fasta33_t -B -S -q -b 100 -H -l /nfs/disk222/yeastpub/bio-soft/fasta/pubseqgbs
-#fastx=-I /nfs/disk222/yeastpub/bio-soft/fasta/fastx33_t -B -S -q -b 40 -H -l /nfs/disk222/yeastpub/bio-soft/fasta/pubseqgbs
 fasta=-I /software/pathogen/external/bin/fasta34_t -B -S -q -b 100 -H -l /software/pathogen/external/etc/pubseqgbs
 fastx=-I /software/pathogen/external/bin/fastx34_t -B -S -q -b 40 -H -l /software/pathogen/external/etc/pubseqgbs
 
-- 
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