diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/fastqc/fastqc_0.11.x.patch')
| -rw-r--r-- | var/spack/repos/builtin/packages/fastqc/fastqc_0.11.x.patch | 30 |
1 files changed, 30 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/fastqc/fastqc_0.11.x.patch b/var/spack/repos/builtin/packages/fastqc/fastqc_0.11.x.patch new file mode 100644 index 0000000000..a0a1155905 --- /dev/null +++ b/var/spack/repos/builtin/packages/fastqc/fastqc_0.11.x.patch @@ -0,0 +1,30 @@ +--- fastqc.orig 2015-11-20 09:25:00.000000000 +0000 ++++ fastqc 2016-10-24 19:06:16.734000000 +0000 +@@ -38,12 +38,21 @@ + $delimiter = ';'; + } + +-if ($ENV{CLASSPATH}) { +- $ENV{CLASSPATH} .= "$delimiter$RealBin$delimiter$RealBin/sam-1.103.jar$delimiter$RealBin/jbzip2-0.9.jar$delimiter$RealBin/cisd-jhdf5.jar"; +-} +-else { +- $ENV{CLASSPATH} = "$RealBin$delimiter$RealBin/sam-1.103.jar$delimiter$RealBin/jbzip2-0.9.jar$delimiter$RealBin/cisd-jhdf5.jar"; +-} ++# The lib dir is $RealBin/../lib ++# start with list of jars we need and prefix them with the lib dir ++# then stick CLASSPATH onto the front (empty or otherwise...) ++# then filter out anything that's empty (perhaps CLASSPATH...) ++# then join all the remainings bits with the delimiter. ++use File::Basename; ++use File::Spec::Functions; ++my $_lib = catfile(dirname($RealBin), 'lib'); ++$ENV{CLASSPATH} = ++ join($delimiter, ++ grep {$_} ++ ($ENV{CLASSPATH}, ++ $_lib, ++ map {"$_lib/$_"} ++ qw(sam-1.103.jar jbzip2-0.9.jar cisd-jhdf5.jar))); + + my @java_args; + my @files; |