diff options
Diffstat (limited to 'biology/snpeff/files/patch-scripts_snpEff')
| -rw-r--r-- | biology/snpeff/files/patch-scripts_snpEff | 27 |
1 files changed, 27 insertions, 0 deletions
diff --git a/biology/snpeff/files/patch-scripts_snpEff b/biology/snpeff/files/patch-scripts_snpEff new file mode 100644 index 000000000000..dace484960d7 --- /dev/null +++ b/biology/snpeff/files/patch-scripts_snpEff @@ -0,0 +1,27 @@ +--- scripts/snpEff.orig 2021-04-13 22:55:13 UTC ++++ scripts/snpEff +@@ -13,9 +13,10 @@ + # Created by: Brad Chapman + #--------------------------------------------------------------------------------------------------- + +-jardir="$(cd "$(dirname "$0")" && cd ".." && pwd -P)" ++jardir=%%JAVAJARDIR%%/snpeff ++userdir=~/snpEff ++JAVA_HOME=%%PREFIX%%/openjdk12 + +-java=java + if [ -e "$JAVA_HOME/bin/java" ] + then + java="$JAVA_HOME/bin/java" +@@ -43,8 +44,9 @@ if [ "$jvm_mem_opts" == "" ]; then + jvm_mem_opts="$default_jvm_mem_opts" + fi + if [[ "$pass_args" != "" && ! "$pass_args" =~ "-c " ]]; then +- pass_args="$pass_args -c ${jardir}/snpEff.config" ++ pass_args="$pass_args -c ${userdir}/snpEff.config" + fi + ++mkdir -p ~/snpEff ++cp ${jardir}/*.config ~/snpEff + exec $java $jvm_mem_opts $jvm_prop_opts -jar ${jardir}/snpEff.jar $pass_args +-exit |