Description: Putting Debian paths for the jars in .sh executables
Author: Pierre Gruet <pgtdebian@free.fr>
Forwarded: not-needed
Last-Update: 2021-02-12

--- a/src/scripts/Drop-seq_alignment.sh
+++ b/src/scripts/Drop-seq_alignment.sh
@@ -114,7 +114,7 @@
 gene_intervals=$(dirname $reference)/$reference_basename.genes.intervals
 exon_intervals=$(dirname $reference)/$reference_basename.exon.intervals
 refflat=$(dirname $reference)/$reference_basename.refFlat
-picard_jar=${dropseq_root}/3rdParty/picard/picard.jar
+picard_jar=/usr/share/java/picard.jar
 
 unmapped_bam=$1
 tagged_unmapped_bam=${tmpdir}/unaligned_mc_tagged_polyA_filtered.bam
--- a/src/scripts/create_Drop-seq_reference_metadata.sh
+++ b/src/scripts/create_Drop-seq_reference_metadata.sh
@@ -118,7 +118,7 @@
 }
 
 function invoke_picard() {
-    check_invoke java -jar $dropseq_root/3rdParty/picard/picard.jar $@
+    check_invoke java -jar /usr/share/java/picard.jar $@
 }
 
 function invoke_dropseq() {
--- a/src/scripts/public_clp_template.sh
+++ b/src/scripts/public_clp_template.sh
@@ -30,7 +30,7 @@
 then source $thisdir/loadDotKits.sh
 fi
 
-jar_deploy_dir=$thisdir/jar
+jar_deploy_dir=/usr/share/java
 verbose=0
 
 USAGE=$(cat << EOF
@@ -72,4 +72,4 @@
 then set -x
 fi
 
-java -Xmx${xmx} -XX:+UseParallelOldGC -XX:ParallelGCThreads=1 -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+HeapDumpOnOutOfMemoryError -Djava.io.tmpdir=$TMPDIR -jar $jar_deploy_dir/dropseq.jar $progname $*
\ No newline at end of file
+java -Xmx${xmx} -XX:+UseParallelOldGC -XX:ParallelGCThreads=1 -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+HeapDumpOnOutOfMemoryError -Djava.io.tmpdir=$TMPDIR -jar $jar_deploy_dir/dropseq.jar $progname $*