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#!/bin/bash -
#
# This script will start ACT on a UNIX system.
#
QUIET=no
usage () {
echo "SYNOPSIS"
echo " Artemis Comparison Tool (ACT): Genome Comparison Tool"
echo "USAGE"
echo " $0 [options] <SEQUENCE_1> <COMPARISON_1_2> <SEQUENCE_2> ..."
echo "OPTIONS"
echo " SEQUENCE An EMBL, GenBank, FASTA, or GFF3 file"
echo " FEATURE An Artemis TAB file, or GFF file"
echo " COMPARISON A BLAST comparison file in tabular format"
echo
echo " -options FILE Read a text file of options from FILE"
echo " -chado Connect to a Chado database (using PGHOST, PGPORT, PGDATABASE, PGUSER environment variables)"
echo
echo " -Dblack_belt_mode=? Keep warning messages to a minimum [true,false]"
echo " -DuserplotX=FILE[,FILE2] For sequence 'X' open one or more userplots"
echo " -DloguserplotX=FILE[,FILE2] For sequence 'X' open one or more userplots, take log(data)"
echo " -DbamX=FILE[,FILE2,...] For sequence 'X' open one or more BAM, CRAM, VCF, or BCF files"
echo " -Dchado=\"h:p/d?u\" Get ACT to open this CHADO database"
echo " -Dread_only Open CHADO database read-only"
echo "EXAMPLES"
echo " % act"
echo " % act af063097.embl af063097_v_b132222.crunch b132222.embl"
echo " % act -Dblack_belt_mode=true -Dbam1=MAL_0h.bam -Dbam2=MAL_7h.bam,var.raw.new.bcf"
echo " % act -Duserplot2=/pathToFile/userPlot"
echo
echo "HOMEPAGE"
echo " http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act"
echo
exit 0
}
# Special Sanger override on chado PGUSER
if [[ "$ARTEMIS_SANGER_DBUSER" != "" ]]
then
export PGUSER=$ARTEMIS_SANGER_DBUSER
fi
#
# Parse arguments.
#
APPLICATION_PROPERTIES="-Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX $SANGER_ARTEMIS_OPTIONS"
while test $# != 0
do
case $1 in
-options) APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dextra_options=$2"; shift ;;
-chado) APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dchado=$PGHOST:$PGPORT/$PGDATABASE?$PGUSER -Dibatis" ;;
-D*) APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES $1" ;;
-quiet) QUIET=yes ; APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Drun_quietly=true" ;;
-help) usage ;;
--help) usage ;;
-h) usage ;;
*) break ;;
esac
shift
done
#
# "-mx2g" sets the maximum amount of memory to use.
# This may need to be increased when dealing with large files
#
if [[ "$ARTEMIS_JVM_FLAGS" = "" ]]
then
FLAGS="-mx2g -ms100m -noverify"
else
FLAGS="$ARTEMIS_JVM_FLAGS -noverify"
fi
#
# Temporary flags to avoid Java 9+ reflection warnings being written to the terminal.
# Should not be necessary when Ibatis is replaced.
#
FLAGS="$FLAGS --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED"
if [[ "$QUIET" = no ]]
then
echo "Starting ACT with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
fi
java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/java/act.jar $*
result=$?
exit $result
|
