Revision 9b6fc2118e06cba65064c7775bb4cf5b0d4bb9a5 authored by Susanna Siebert on 15 June 2015, 20:44:01 UTC, committed by Susanna Siebert on 15 June 2015, 20:44:01 UTC
Check that the md5 file exists after the merged speedseq alignment result gets created
genome_view_dev.sh
#!/gsc/bin/bash
#
# This script is used by /etc/init.d/genome_view on imp and aims-dev
# to start the fastcgi daemon. It is here (vs the init script) so apipe
# can update it to change options.
#
MYINC=/gscuser/jlolofie/dev/git/genome_untouched/lib/perl
INC=/gsc/scripts/opt/genome/current/web/lib/perl
export XGENOME_DEV_MODE=0
## change the symlink to the real path
INC=`cd $INC; pwd -P`
## this must be the same as /etc/init.d/genome_view
PIDFILE="/var/run/kom_fastcgi/genome_view.pid"
if test ! -w $PIDFILE
then
rm -f $PIDFILE
fi
echo $$ >$PIDFILE
LOGFILE=/var/log/kom/genome_view.log
## other options
PSGI=$MYINC/Genome/Model/Command/Services/WebApp/Main.psgi
PORT=3060
WORKERS=20
OPTIONS="-M Genome::Model::Command::Services::WebApp::FCGI::Patch --app $PSGI --server FCGI -E development -I $MYINC -I $INC --port $PORT -M Genome::Model::Command::Services::WebApp::Core --nproc $WORKERS --keep-stderr 1 --manager Genome::Model::Command::Services::WebApp::FCGI::ProcManager --pid $PIDFILE"
# override perl5lib to be exactly what we want, no more
PERL5LIB=/gsc/scripts/opt/genome/vendor/lib/perl5:/gsc/scripts/lib/perl
export PERL5LIB
export XGENOME_VIEW_CACHE=1
echo "starting server from $0 with XGENOME_DEV_MODE=$XGENOME_DEV_MODE" >>$LOGFILE
exec /gsc/bin/plackup $OPTIONS >>$LOGFILE 2>&1
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