Permalink
Find file
Fetching contributors…
Cannot retrieve contributors at this time
executable file 133 lines (100 sloc) 3.11 KB
#!/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: /cvsroot/pathsoft/artemis/etc/run_tblastx,v 1.4 2005-12-20 13:50:10 tjc Exp $"
cleanUp()
{
echo $1
cat $1 | while thisLine=`line`
do
rm -f $thisLine
done
rm -f $1
}
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
DIRNAME=$4
### change these lines:
EXEC=${EXEC-`which blastall 2>/dev/null`}
if [ ! -x "$EXEC" ]; then
EXEC=`find Artemis* -name blastall 2>/dev/null`
fi
if [ ! -d "$BLASTDB" ]; then
DATABASE_TMP="$PWD/"`find Artemis* -name blast-data 2>/dev/null`"/$DATABASE"
if [ -f "$DATABASE_TMP" ]; then
DATABASE="$DATABASE_TMP"
fi
fi
echo "about to start $EXEC with input from $INPUT_FILE and output to" 1>&2
echo "$OUTPUT_FILE using database $DATABASE" 1>&2
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 tblastx \
# $EXTRA_ARGS >! $OUTPUT_FILE"
rsh babel "cd $WDIR; bsub -q longblastq -o $OUTPUT_FILE -e ${PROG}_errors.new -I flexi_blast.pl -tx $DATABASE $INPUT_FILE $EXTRA_ARGS"
else
# lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p tblastx \
# $EXTRA_ARGS 2>&1 > $OUTPUT_FILE |
# tee ${PROG}_errors.new 1>&2
bsub -q long -o $OUTPUT_FILE -e ${PROG}_errors.new -I flexi_blast.pl -tx $DATABASE $INPUT_FILE $EXTRA_ARGS
fi
#### end of changes
# Artemis can read compressed files
count=0; while (test ! -f $OUTPUT_FILE) && (test $count -lt 1000) ; do sleep 2; count+=1; done
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
gzip -9 $OUTPUT_FILE
zip -j ${DIRNAME}tblastx.zip ${OUTPUT_FILE}.gz
rm -f ${OUTPUT_FILE}.gz
}
(echo "#!/bin/sh -"; echo "kill $$") > $PROG.kill
chmod a+x $PROG.kill
DIR=`dirname $PWD/$1`
if [ x$ONEFILE = x ]
then
for i in `cat $1`
do
run_one_prog $i $i.out $EXPANDED_DATABASE "$DIR/"
done
else
run_one_prog $1 $2 $EXPANDED_DATABASE "$DIR/"
fi
cleanUp $1
exit 0