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Commit 393dd0f2 authored by tjc's avatar tjc
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fixes for macosx app

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@3943 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent 3c642d62
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......@@ -6,7 +6,7 @@
# to customise this script see the function called run_one_prog below
RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastn,v 1.3 2005-02-21 11:42:46 tjc Exp $"
RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastn,v 1.4 2005-12-20 13:49:49 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
......@@ -41,7 +41,18 @@ run_one_prog () {
### change these lines:
EXEC=blastall
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 $INPUT_FILE and output to"
echo "$OUTPUT_FILE using database $DATABASE"
......
......@@ -6,7 +6,7 @@
# to customise this script see the function called run_one_prog below
RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastx,v 1.3 2005-02-21 11:46:53 tjc Exp $"
RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastx,v 1.4 2005-12-20 13:49:57 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
......@@ -41,7 +41,18 @@ run_one_prog () {
### change these lines:
EXEC=blastall
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 $INPUT_FILE and output to"
echo "$OUTPUT_FILE using database $DATABASE"
......
......@@ -6,7 +6,7 @@
# to customise this script see the function called run_one_prog below
RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_tblastn,v 1.2 2004-10-05 16:08:05 tjc Exp $"
RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_tblastn,v 1.3 2005-12-20 13:50:05 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
......@@ -41,7 +41,18 @@ run_one_prog () {
### change these lines:
EXEC=blastall
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 $DATABASE" 1>&2
......
......@@ -6,7 +6,7 @@
# to customise this script see the function called run_one_prog below
RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_tblastx,v 1.3 2005-06-09 13:40:12 tjc Exp $"
RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_tblastx,v 1.4 2005-12-20 13:50:10 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
......@@ -41,7 +41,18 @@ run_one_prog () {
### change these lines:
EXEC=blastall
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
......
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