diff options
Diffstat (limited to 'biology/gatk/files/gatk.sh.in')
| -rw-r--r-- | biology/gatk/files/gatk.sh.in | 4 |
1 files changed, 2 insertions, 2 deletions
diff --git a/biology/gatk/files/gatk.sh.in b/biology/gatk/files/gatk.sh.in index d3d5c0f7bf5a..20c6c16d5164 100644 --- a/biology/gatk/files/gatk.sh.in +++ b/biology/gatk/files/gatk.sh.in @@ -23,5 +23,5 @@ fi # execute the command # add the LIBBWA_PATH system parameter (not sure whether the env. var or argument alone are sufficient) -JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so" \ -%%JAVA%% $MEM_OPTS -DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -jar %%JAVAJARDIR%%/GenomeAnalysisTK-%%PORTVERSION%%.jar "$@" +JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -DLIBFML_PATH=%%PREFIX%%/lib/libfml.so" \ +%%JAVA%% $MEM_OPTS -DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -DLIBFML_PATH=%%PREFIX%%/lib/libfml.so -jar %%JAVAJARDIR%%/GenomeAnalysisTK-%%PORTVERSION%%.jar "$@" |