zip blastx results

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13760 ee4ac58c-ac51-4696-9907-e4b3aa274f04

etc/run_blastx.sanger

@@ -6,7 +6,17 @@
 # to customise this script see the function called run_one_prog below
 
 
-RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastx.sanger,v 1.2 2005-07-11 15:06:21 tjc Exp $"
+RCS_HEADER="$Header: /cvsroot/pathsoft/artemis/etc/run_blastx.sanger,v 1.2 2005/07/11 15:06:21 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/'`
 
@@ -27,18 +37,21 @@ else
     fi
 fi
 
+if [ $DATABASE = "psu/Kineto_aa" ]; then
+  BLASTDB=/lustre/pathogen/blast; export BLASTDB
+fi
 
 # expand any ~ or environment variables
 EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
 
-
+echo $BLASTDB
 ### change this function to suit your site:
 
 run_one_prog () {
     INPUT_FILE=$1
     OUTPUT_FILE=$2
     DATABASE=$3
-
+    DIRNAME=$4
 
     ### change these lines:
     EXEC=blastall
@@ -66,44 +79,43 @@ run_one_prog () {
       rsh babel "cd $WDIR; lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastx \
                             $EXTRA_ARGS >! $OUTPUT_FILE"
     else
-      bsub -q  longblastq -o $OUTPUT_FILE -e ${PROG}_errors.new -I flexi_blast.pl -x $DATABASE $INPUT_FILE $EXTRA_ARGS
-#     lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastx \
-#         $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 -x $DATABASE $INPUT_FILE $EXTRA_ARGS
     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
+    while [ ! -f $OUTPUT_FILE ]; do sleep 2; done
+
+    gzip -9 $OUTPUT_FILE
+    zip -j ${DIRNAME}blastx.zip ${OUTPUT_FILE}.gz
+    rm -f ${OUTPUT_FILE}.gz
+
+#   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
+DIR=`dirname $PWD/$1`
 
 if [ x$ONEFILE = x ]
 then
     for i in `cat $1`
     do
-        run_one_prog $i $i.out $EXPANDED_DATABASE
+        run_one_prog $i $i.out $echo $EXPANDED_DATABASE "$DIR/"
     done
 
 else
-    run_one_prog $1 $2 $EXPANDED_DATABASE
+    run_one_prog $1 $2 $EXPANDED_DATABASE "$DIR/"
 fi
 
+cleanUp $1
 exit 0