diff --git a/etc/run_blastn.sanger b/etc/run_blastn.sanger
new file mode 100755
index 0000000000000000000000000000000000000000..da0f6b949f63243c449027b2e7c2e297000f0c62
--- /dev/null
+++ b/etc/run_blastn.sanger
@@ -0,0 +1,108 @@
+#!/bin/sh -
+
+# this script will run a search program on a sequence input file or on each
+# file in a file of filenames
+
+# to customise this script see the function called run_one_prog below
+
+
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastn.sanger,v 1.1 2005-02-21 11:42:18 tjc Exp $"
+
+PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
+
+
+if [ $# = 4 -a x$1 = x-onefile ]
+then
+ shift
+ ONEFILE=t
+ DATABASE=$3 export DATABASE
+else
+ if [ $# = 2 ]
+ then
+ DATABASE=$2 export DATABASE
+ else
+ echo usage: $0 -onefile input_file output_file database
+ echo or: $0 file_of_filenames database
+ exit 1
+ fi
+fi
+
+
+# expand any ~ or environment variables
+EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
+
+
+### change this function to suit your site:
+
+run_one_prog () {
+ INPUT_FILE=$1
+ OUTPUT_FILE=$2
+ DATABASE=$3
+
+
+ ### change these lines:
+ EXEC=blastall
+
+ echo "about to start $EXEC with input from $INPUT_FILE and output to"
+ echo "$OUTPUT_FILE using database $DATABASE"
+
+
+ EXTRA_ARGS=
+
+ # add/change the flags to suit your site:
+
+ HOSTNAME=`hostname`
+ REMOTE=N
+
+ case $HOSTNAME in
+ deskpro*)
+ REMOTE=Y ;;
+ *)
+ esac
+
+ if [ $REMOTE = "Y" ]; then
+ WDIR=`pwd`
+ export WDIR
+ rsh babel "cd $WDIR; lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastn \
+ $EXTRA_ARGS >! $OUTPUT_FILE"
+ else
+ lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastn \
+ $EXTRA_ARGS 2>&1 > $OUTPUT_FILE |
+ tee ${PROG}_errors.new 1>&2
+ fi
+
+# lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastn \
+# $EXTRA_ARGS 2>&1 > $OUTPUT_FILE |
+# tee ${PROG}_errors.new 1>&2
+
+ #### end of changes
+
+
+ # Artemis can read compressed files
+ gzip -9 $OUTPUT_FILE &
+
+ if [ -s ${PROG}_errors.new ]
+ then
+ ( echo ERROR running $PROG: ; echo;
+ echo ===================================================
+ cat ${PROG}_errors.new ) >> $OUTPUT_FILE
+ cat ${PROG}_errors.new >> ${PROG}_errors
+ fi
+}
+
+(echo "#!/bin/sh -"; echo "kill $$") > $PROG.kill
+
+chmod a+x $PROG.kill
+
+if [ x$ONEFILE = x ]
+then
+ for i in `cat $1`
+ do
+ run_one_prog $i $i.out $EXPANDED_DATABASE
+ done
+
+else
+ run_one_prog $1 $2 $EXPANDED_DATABASE
+fi
+
+exit 0
diff --git a/etc/run_blastp.sanger b/etc/run_blastp.sanger
new file mode 100755
index 0000000000000000000000000000000000000000..b97b1d98cec72b2a07eafb5f1e7c3beaa10f556c
--- /dev/null
+++ b/etc/run_blastp.sanger
@@ -0,0 +1,111 @@
+#!/bin/sh -
+
+# this script will run a search program on a sequence input file or on each
+# file in a file of filenames
+
+# to customise this script see the function called run_one_prog below
+
+
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastp.sanger,v 1.1 2005-02-21 11:45:09 tjc Exp $"
+
+PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
+
+#BLASTDB=/data/blastdb
+#BLASTMAT=/data/blastdb/aa
+#export BLASTDB
+#export BLASTMAT
+
+if [ $# = 4 -a x$1 = x-onefile ]
+then
+ shift
+ ONEFILE=t
+ DATABASE=$3 export DATABASE
+else
+ if [ $# = 2 ]
+ then
+ DATABASE=$2 export DATABASE
+ else
+ echo usage: $0 -onefile input_file output_file database
+ echo or: $0 file_of_filenames database
+ exit 1
+ fi
+fi
+
+
+# expand any ~ or environment variables
+EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
+
+
+### change this function to suit your site:
+
+run_one_prog () {
+ INPUT_FILE=$1
+ OUTPUT_FILE=$2
+ DATABASE=$3
+
+
+ ### change these lines:
+ EXEC=blastall
+
+ echo "about to start $EXEC with input from $INPUT_FILE and output to"
+ echo "$OUTPUT_FILE using database $DATABASE"
+
+
+ EXTRA_ARGS=
+
+ HOSTNAME=`hostname`
+ REMOTE=N
+
+ case $HOSTNAME in
+ deskpro*)
+ REMOTE=Y ;;
+ *)
+ esac
+
+ if [ $REMOTE = "Y" ]; then
+ WDIR=`pwd`
+ export WDIR
+ rsh babel "cd $WDIR; lsrun -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -v \
+ blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastp \
+ $EXTRA_ARGS >! $OUTPUT_FILE"
+ else
+ # add/change the flags to suit your site:
+ lsrun -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -v \
+ blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastp \
+ $EXTRA_ARGS 2>&1 > $OUTPUT_FILE |
+ tee ${PROG}_errors.new 1>&2
+ fi
+
+ #### end of changes
+
+
+ # Artemis can read compressed files
+ gzip -9 $OUTPUT_FILE &
+
+ if [ -s ${PROG}_errors.new ]
+ then
+ ( echo ERROR running $PROG: ; echo;
+ echo ===================================================
+ cat ${PROG}_errors.new ) >> $OUTPUT_FILE
+ cat ${PROG}_errors.new >> ${PROG}_errors
+ fi
+}
+
+(echo "#!/bin/sh -"; echo "kill $$") > $PROG.kill
+
+chmod a+x $PROG.kill
+
+echo $1
+if [ x$ONEFILE = x ]
+then
+ for i in `cat $1`
+ do
+ echo "run_one_prog $i $i.out $EXPANDED_DATABASE"
+ run_one_prog $i $i.out $EXPANDED_DATABASE
+ done
+
+else
+ run_one_prog $1 $2 $EXPANDED_DATABASE
+fi
+
+exit 0
diff --git a/etc/run_blastx.sanger b/etc/run_blastx.sanger
new file mode 100755
index 0000000000000000000000000000000000000000..53b525748ab9f7720fbc33277323c9d0aaf2efa8
--- /dev/null
+++ b/etc/run_blastx.sanger
@@ -0,0 +1,108 @@
+#!/bin/sh -
+
+# this script will run a search program on a sequence input file or on each
+# file in a file of filenames
+
+# to customise this script see the function called run_one_prog below
+
+
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastx.sanger,v 1.1 2005-02-21 11:46:35 tjc Exp $"
+
+PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
+
+
+if [ $# = 4 -a x$1 = x-onefile ]
+then
+ shift
+ ONEFILE=t
+ DATABASE=$3 export DATABASE
+else
+ if [ $# = 2 ]
+ then
+ DATABASE=$2 export DATABASE
+ else
+ echo usage: $0 -onefile input_file output_file database
+ echo or: $0 file_of_filenames database
+ exit 1
+ fi
+fi
+
+
+# expand any ~ or environment variables
+EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
+
+
+### change this function to suit your site:
+
+run_one_prog () {
+ INPUT_FILE=$1
+ OUTPUT_FILE=$2
+ DATABASE=$3
+
+
+ ### change these lines:
+ EXEC=blastall
+
+ echo "about to start $EXEC with input from $INPUT_FILE and output to"
+ echo "$OUTPUT_FILE using database $DATABASE"
+
+
+ EXTRA_ARGS=
+
+ # add/change the flags to suit your site:
+
+ HOSTNAME=`hostname`
+ REMOTE=N
+
+ case $HOSTNAME in
+ deskpro*)
+ REMOTE=Y ;;
+ *)
+ esac
+
+ if [ $REMOTE = "Y" ]; then
+ WDIR=`pwd`
+ export WDIR
+ rsh babel "cd $WDIR; lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastx \
+ $EXTRA_ARGS >! $OUTPUT_FILE"
+ else
+ lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastx \
+ $EXTRA_ARGS 2>&1 > $OUTPUT_FILE |
+ tee ${PROG}_errors.new 1>&2
+ fi
+
+# lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastx \
+# $EXTRA_ARGS 2>&1 > $OUTPUT_FILE |
+# tee ${PROG}_errors.new 1>&2
+
+ #### end of changes
+
+
+ # Artemis can read compressed files
+ gzip -9 $OUTPUT_FILE &
+
+ if [ -s ${PROG}_errors.new ]
+ then
+ ( echo ERROR running $PROG: ; echo;
+ echo ===================================================
+ cat ${PROG}_errors.new ) >> $OUTPUT_FILE
+ cat ${PROG}_errors.new >> ${PROG}_errors
+ fi
+}
+
+(echo "#!/bin/sh -"; echo "kill $$") > $PROG.kill
+
+chmod a+x $PROG.kill
+
+if [ x$ONEFILE = x ]
+then
+ for i in `cat $1`
+ do
+ run_one_prog $i $i.out $EXPANDED_DATABASE
+ done
+
+else
+ run_one_prog $1 $2 $EXPANDED_DATABASE
+fi
+
+exit 0
diff --git a/etc/run_clustalx.sanger b/etc/run_clustalx.sanger
new file mode 100755
index 0000000000000000000000000000000000000000..f2714f434334c9e7bc49fec5c6392ac9f0435c5b
--- /dev/null
+++ b/etc/run_clustalx.sanger
@@ -0,0 +1,59 @@
+#!/bin/sh -
+
+# this script will run clustalx on a temporary file containing the concatenated
+# contents of files listed in a file of filenames
+
+
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_clustalx.sanger,v 1.1 2005-02-21 11:49:41 tjc Exp $"
+
+PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
+
+
+if [ $# != 1 ]
+then
+ echo usage: $0 file_of_filenames
+fi
+
+(echo "#!/bin/sh -"; echo "kill $$") > $PROG.kill
+
+chmod a+x $PROG.kill
+
+file_of_filenames=$1
+date=`date +"%y_%m_%d"`
+hostname=`hostname`
+temp_file_name=clustalx/artemis_temp.$$.$hostname.$date.clustalx_input.fasta
+
+cat $file_of_filenames | xargs cat > $temp_file_name
+
+# make sure that the identifiers are unique for clustalx
+perl -pne 'if (/^>(\S+)/) {
+ $name = $1;
+ if (exists $h{$name}) {
+ $i = $h{$name}++;
+ s/^>(\S+)/>$name.$i/;
+ } else {
+ $h{$name} = 0;
+ }
+}' $temp_file_name > $temp_file_name.processed
+
+# delete it at some point
+echo "rm -f $temp_file_name* > /dev/null 2>&1" | at now + 8 hours
+
+HOSTNAME=`hostname`
+REMOTE=N
+
+case $HOSTNAME in
+ deskpro*)
+ REMOTE=Y ;;
+ *)
+esac
+
+if [ $REMOTE = "Y" ]; then
+ WDIR=`pwd`
+ export WDIR
+ ssh babel "cd $WDIR; clustalx $temp_file_name.processed"
+else
+ clustalx $temp_file_name.processed
+fi
+
+exit 0
diff --git a/etc/run_fasta.sanger b/etc/run_fasta.sanger
new file mode 100755
index 0000000000000000000000000000000000000000..091365b724333fd86a8fb85fd69bd3238cfb347f
--- /dev/null
+++ b/etc/run_fasta.sanger
@@ -0,0 +1,198 @@
+#!/bin/sh -
+
+# this script will run a search program on a sequence input file or on each
+# file in a file of filenames
+
+# to customise this script see the function called run_one_prog below
+
+
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_fasta.sanger,v 1.1 2005-02-21 11:51:10 tjc Exp $"
+
+PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
+
+
+if [ $# = 4 -a x$1 = x-onefile ]
+then
+ shift
+ ONEFILE=t
+ DATABASE=$3 export DATABASE
+else
+ if [ $# = 2 ]
+ then
+ DATABASE=$2 export DATABASE
+ else
+ echo usage: $0 -onefile input_file output_file database 1>&2
+ echo or: $0 file_of_filenames database 1>&2
+ exit 1
+ fi
+fi
+
+
+#
+# Exchange DB name for fasta reference
+#
+if [ "$DATABASE" = "%uniprot" ]; then
+ DATABASE="%U";
+elif [ "$DATABASE" = "%uniprot_archaea" ]; then
+ DATABASE="%A";
+elif [ "$DATABASE" = "%uniprot_bacteria" ]; then
+ DATABASE="%B";
+elif [ "$DATABASE" = "%uniprot_eukaryota" ]; then
+ DATABASE="%E";
+elif [ "$DATABASE" = "%uniprot_viruses" ]; then
+ DATABASE="%V";
+elif [ "$DATABASE" = "%uniprot_rest" ]; then
+ DATABASE="%R";
+elif [ "$DATABASE" = "%malaria" ]; then
+ DATABASE="%M";
+elif [ "$DATABASE" = "%kineto_aa" ]; then
+ DATABASE="%K";
+fi
+
+# expand any ~ or environment variables
+EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
+
+### change this function to suit your site:
+
+run_one_prog () {
+ INPUT_FILE=$1
+ OUTPUT_FILE=$2
+ DATABASE=$3
+
+### strip out directory from command line
+
+ IN=`echo $INPUT_FILE | sed -n -e "s|$PWD//||p"`
+
+ if test "$IN" != "" && test -f $IN; then
+ INPUT_FILE="$IN"
+ fi
+
+ echo "\n\nIN=$IN\nPWD=$PWD\nINPUT_FILE=$INPUT_FILE\n\n"
+ ### change these lines:
+
+ ### get sequence size
+ seq_size=`infoseq "$INPUT_FILE" -length -only -auto | awk '{ sum += $1 } END { print sum }`
+
+ FASTLIBS=/nfs/disk222/yeastpub/bio-soft/fasta/pubseqgbs export FASTLIBS
+ EXEC=/nfs/disk222/yeastpub/bio-soft/fasta/fasta33_t
+
+ echo "about to start $EXEC with input from $INPUT_FILE and output to" 1>&2
+ echo "$OUTPUT_FILE using database $DATABASE" 1>&2
+
+ # add/change the flags to suit your site:
+ COMMAND="$EXEC -B -S -q -b 100 -H $INPUT_FILE $DATABASE ktup 2"
+
+ echo "command line: $COMMAND" 1>&2
+
+# lsrun -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -v $COMMAND 2>&1 > $OUTPUT_FILE |
+
+ if [ "$seq_size" -lt 50000 ]
+ then
+ bsub -q normal -n 1 -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -I $COMMAND 2>&1 > $OUTPUT_FILE |
+ tee ${PROG}_errors.new 1>&2
+ else
+ bsub -q "longblastq" -n 1 -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -I $COMMAND 2>&1 > $OUTPUT_FILE |
+ tee ${PROG}_errors.new 1>&2
+ fi
+
+ #### end of changes
+
+
+ # Artemis can read compressed files
+ gzip -9 $OUTPUT_FILE &
+
+ if [ -s ${PROG}_errors.new ]
+ then
+ ( echo ERROR running $PROG: ; echo;
+ echo ===================================================
+ cat ${PROG}_errors.new ) >> $OUTPUT_FILE
+ cat ${PROG}_errors.new >> ${PROG}_errors
+ fi
+}
+
+PERL_PROG='
+
+local *BSUB;
+
+my $file = $ARGV[0];
+my $database = $ARGV[1];
+my $pwd = $ARGV[2];
+chomp $file;
+chomp $database;
+
+$ENV{'FASTLIBS'} = "/nfs/disk222/yeastpub/bio-soft/fasta/pubseqgbs_test";
+
+
+open(BSUB, "| bsub -q normal -o fasta_errors -n 1 -R \"select[blast && mem > 500] rusage[r1m=1:mem=500]\" -K") or die "could not open bsub pipe : $!";
+open(LIST_FILE,$file);
+
+$EXEC="/nfs/disk222/yeastpub/bio-soft/fasta/fasta33_t";
+
+while(my $inFile = <LIST_FILE>)
+{
+ chomp($inFile);
+
+ if($inFile =~ m/^($pwd)(.*)/)
+ {
+ my $inFile_tmp = $2;
+ while($inFile_tmp =~ m/^(\/)(.*)/)
+ {
+ $inFile_tmp = $2;
+ }
+
+ if( -e $inFile_tmp )
+ {
+ $inFile = $inFile_tmp;
+ }
+ }
+
+ if($inFile =~ m/^(\S{100})/)
+ {
+ if($inFile =~ m/^(\S{90,})(fasta\/\S+)/)
+ {
+ my $inFile_tmp = $1;
+
+ if( -e $inFile_tmp )
+ {
+ print BSUB "cd $inFile_tmp\n";
+ $inFile = $2;
+ }
+ }
+ }
+
+ print BSUB "$EXEC -B -S -q -b 100 -H $inFile $database ktup 2 > $inFile\.out\n";
+ print BSUB "gzip -9 $inFile\.out\n";
+}
+close BSUB or die "--Could not submit job : $!";
+close LIST_FILE;
+
+'
+
+(echo "#!/bin/sh -"; echo "kill $$") > $PROG.kill
+
+chmod a+x $PROG.kill
+
+HOSTNAME=`hostname`
+REMOTE=N
+
+case $HOSTNAME in
+ deskpro*)
+ REMOTE=Y ;;
+ *)
+esac
+
+if [ x$ONEFILE = x ]
+then
+ if [ $REMOTE = "Y" ]; then
+ WDIR=`pwd`
+ export WDIR
+ CMD=`echo $PERL_PROG`
+ rsh babel "cd $WDIR; perl -w -e '$CMD' \"$1\" \"$EXPANDED_DATABASE\" \"$PWD\""
+ else
+ perl -w -e "$PERL_PROG" "$1" "$EXPANDED_DATABASE" "$PWD"
+ fi
+else
+ run_one_prog $1 $2 $EXPANDED_DATABASE
+fi
+
+exit 0
diff --git a/etc/run_fastx.sanger b/etc/run_fastx.sanger
new file mode 100644
index 0000000000000000000000000000000000000000..120492493a44ee35af5e545c2810246f34e721a0
--- /dev/null
+++ b/etc/run_fastx.sanger
@@ -0,0 +1,103 @@
+#!/bin/sh -
+
+# this script will run a search program on a sequence input file or on each
+# file in a file of filenames
+
+# to customise this script see the function called run_one_prog below
+
+
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_fastx.sanger,v 1.1 2005-02-21 11:53:49 tjc Exp $"
+
+PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
+
+
+if [ $# = 4 -a x$1 = x-onefile ]
+then
+ shift
+ ONEFILE=t
+ DATABASE=$3 export DATABASE
+else
+ if [ $# = 2 ]
+ then
+ DATABASE=$2 export DATABASE
+ else
+ echo usage: $0 -onefile input_file output_file database 1>&2
+ echo or: $0 file_of_filenames database 1>&2
+ exit 1
+ fi
+fi
+
+
+# expand any ~ or environment variables
+EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
+
+
+### change this function to suit your site:
+
+run_one_prog () {
+ INPUT_FILE=$1
+ OUTPUT_FILE=$2
+ DATABASE=$3
+
+
+ ### change these lines:
+
+ FASTLIBS=/nfs/disk222/yeastpub/bio-soft/fasta/pubseqgbs export FASTLIBS
+ EXEC=/nfs/disk222/yeastpub/bio-soft/fasta/fastx33_t
+
+ echo "about to start $EXEC with input from $INPUT_FILE and output to" 1>&2
+ echo "$OUTPUT_FILE using database $DATABASE" 1>&2
+
+ # add/change the flags to suit your site:
+ HOSTNAME=`hostname`
+ REMOTE=N
+
+ case $HOSTNAME in
+ deskpro*)
+ REMOTE=Y ;;
+ *)
+ esac
+
+ COMMAND="$EXEC -B -S -q -b 40 -H $INPUT_FILE $DATABASE ktup 2"
+ echo "command line: $COMMAND" 1>&2
+
+ if [ $REMOTE = "Y" ]; then
+ WDIR=`pwd`
+ export WDIR
+ rsh babel "cd $WDIR; $COMMAND >! $OUTPUT_FILE"
+ else
+ $COMMAND 2>&1 > $OUTPUT_FILE |
+ tee ${PROG}_errors.new 1>&2
+ fi
+
+ #### end of changes
+
+
+ # Artemis can read compressed files
+ gzip -9 $OUTPUT_FILE &
+
+ if [ -s ${PROG}_errors.new ]
+ then
+ ( echo ERROR running $PROG: ; echo;
+ echo ===================================================
+ cat ${PROG}_errors.new ) >> $OUTPUT_FILE
+ cat ${PROG}_errors.new >> ${PROG}_errors
+ fi
+}
+
+(echo "#!/bin/sh -"; echo "kill $$") > $PROG.kill
+
+chmod a+x $PROG.kill
+
+if [ x$ONEFILE = x ]
+then
+ for i in `cat $1`
+ do
+ run_one_prog $i $i.out $EXPANDED_DATABASE
+ done
+
+else
+ run_one_prog $1 $2 $EXPANDED_DATABASE
+fi
+
+exit 0