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Author: Andreas Tille <tille@debian.org>
Last-Update: Mon, 21 Jan 2019 09:01:19 +0100
Description: There is no point in delivering read_file_names in /usr/bin
It is available in /usr/share/discosnp/bin/read_file_names - this patch adapts
the scripts using it.
.
Some other issues of these scripts are fixed as well.
--- a/run_discoSnp++.sh
+++ b/run_discoSnp++.sh
@@ -66,7 +66,8 @@ e="" # if set to -e: Map variant predict
graph_reused="Egg62hdS7knSFvF3" # with -g option, we use a previously created graph.
#EDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
-EDIR=$( python -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) # as suggested by Philippe Bordron
+#EDIR=$( python -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) # as suggested by Philippe Bordron
+EDIR="/usr"
if [ -d "$EDIR/build/" ] ; then # VERSION SOURCE COMPILED
@@ -75,13 +76,13 @@ if [ -d "$EDIR/build/" ] ; then # VERSIO
kissnp2_bin=$EDIR/build/bin/kissnp2
kissreads2_bin=$EDIR/build/bin/kissreads2
else # VERSION BINARY
- read_file_names_bin=$EDIR/bin/read_file_names
+ read_file_names_bin=/usr/lib/discosnp/bin/read_file_names
dbgh5_bin=$EDIR/bin/dbgh5
kissnp2_bin=$EDIR/bin/kissnp2
kissreads2_bin=$EDIR/bin/kissreads2
fi
-chmod +x $EDIR/scripts/*.sh $EDIR/run_discoSnpRad.sh 2>/dev/null # Usefull for binary distributions
+#chmod +x $EDIR/scripts/*.sh $EDIR/run_discoSnpRad.sh 2>/dev/null # Usefull for binary distributions
useref=""
wraith="false"
@@ -685,7 +686,7 @@ echo -e " #################### CREATE VC
echo -e " ############################################################### $reset"
if [ -z "$genome" ]; then # NO reference genome use, vcf creator mode 1
- vcfCreatorCmd="$EDIR/scripts/run_VCF_creator.sh -p ${kissprefix}_coherent.fa -o ${kissprefix}_coherent.vcf"
+ vcfCreatorCmd="/usr/share/discosnp/scripts/run_VCF_creator.sh -p ${kissprefix}_coherent.fa -o ${kissprefix}_coherent.vcf"
echo $green$vcfCreatorCmd$cyan
if [[ "$wraith" == "false" ]]; then
$vcfCreatorCmd
@@ -696,7 +697,7 @@ if [ -z "$genome" ]; then # NO referenc
exit 1
fi
else # A Reference genome is provided, vcf creator mode 2
- vcfCreatorCmd="$EDIR/scripts/run_VCF_creator.sh $bwa_path_option -G $genome $bwa_path_option -p ${kissprefix}_coherent.fa -o ${kissprefix}_coherent.vcf -I $option_cores_post_analysis $e"
+ vcfCreatorCmd="/usr/share/discosnp/scripts/run_VCF_creator.sh $bwa_path_option -G $genome $bwa_path_option -p ${kissprefix}_coherent.fa -o ${kissprefix}_coherent.vcf -I $option_cores_post_analysis $e"
echo $green$vcfCreatorCmd$cyan
if [[ "$wraith" == "false" ]]; then
$vcfCreatorCmd
@@ -729,4 +730,4 @@ if [[ "$wraith" == "false" ]]; then
fi
echo -e " Thanks for using discoSnp++ - http://colibread.inria.fr/discoSnp/ - Forum: http://www.biostars.org/t/discoSnp/"
echo -e "################################################################################################################$reset"
-fi
\ No newline at end of file
+fi
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