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--- fastqc.orig 2023-05-26 08:02:49.123718275 +0100
+++ fastqc 2023-05-26 08:12:19.980320240 +0100
@@ -38,13 +38,21 @@
$delimiter = ';';
}
-if ($ENV{CLASSPATH}) {
- $ENV{CLASSPATH} .= "$delimiter$RealBin$delimiter$RealBin/htsjdk.jar$delimiter$RealBin/jbzip2-0.9.jar$delimiter$RealBin/cisd-jhdf5.jar";
-}
-else {
- $ENV{CLASSPATH} = "$RealBin$delimiter$RealBin/htsjdk.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(htsjdk.jar jbzip2-0.9.jar cisd-jhdf5.jar)));
# We need to find the java interpreter. We'll start from the assumption that this
# is included in the path.
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