add comments and generic default options

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@4120 ee4ac58c-ac51-4696-9907-e4b3aa274f04

lib/j2ssh/j2ssh.properties

+#
+#
+# Configuration file for using SSH file management and
+# database searches. 
+# 
+#
+# default login options
 port=2222
 host=localhost
-bsub=bsub -q  longblastq -n 1 -R 'select[blast && mem > 500] rusage[mem=500]' 
+#
+#
+# Sanger options
+# 
+bsub=bsub -q normal -n 1 -R 'select[blast && mem > 500] rusage[mem=500]' 
 blastp=-I /nfs/pathsoft/prod/perl/flexi_blast.pl -p 
 blastx=-I /nfs/pathsoft/prod/perl/flexi_blast.pl -x
 tblastx=-I /nfs/pathsoft/prod/perl/flexi_blast.pl -tx
 blastn=-I /nfs/pathsoft/prod/perl/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
+#
+#
+# Generic default options 
+#
+#blastp=blastall -p blastp
+#blastx=blastall -p blastx
+#tblastx=blastall -p tblastx
+#blastn=blastall -p blastn
+#fasta=fasta33_t -B -S -q -b 100 -H -l /nfs/disk222/yeastpub/bio-soft/fasta/pubseqgbs
+#fastx=fastx33_t -B -S -q -b 40 -H -l /nfs/disk222/yeastpub/bio-soft/fasta/pubseqgbs
+#
+#
+# default working directory
 wdir=/nfs/pathscratch1/scratch
+#
+# 
+# aliases used for fasta
 %uniprot=%U
 %uniprot_archaea=%A
 %uniprot_bacteria=%B
@@ -17,7 +44,11 @@ wdir=/nfs/pathscratch1/scratch
 %malaria=%M
 %kineto_aa=%K
 default_db=%uniprot_bacteria
+#
+#
+# remote directories to use as roots in the file manager
 remotedir.PD=/nfs/pathdata
 remotedir.YP=/nfs/disk222/yeastpub
+# local directories to use as roots in the file manager
 localdir.PD=/nfs/pathdata
 localdir.YP=/nfs/disk222/yeastpub