6e1b3f621d
* Add package for fastqc This tool is a java mess. Their Way To Do It is to just copy the entire tree into it's final resting place, make the perl script at the top level executable and take it from there. Yuck. This package assumes that `set_executable` actually sets all the user bits. If that change doesn't go in, then something equivalent needs to be done. * Use chmod to make fastqc executable I haven't gotten any feedback on changing set-executable, so switch to using chmod (from the cuda package). * Flake8 cleanup * Install files neatly, don't just copy top level of dir Rather than blindly copying everything in the distribution, carefully put the necessary bits into reasonable places. Neatness counts, etc... This requires patching the `fastqc` perl script, so this commit adds a patch file. * Additional pep8 cleanup * Let dependency handle adding jdk to PATH * Flake8 cleanup * Ensure that java is on PATH I thought that the run dependency on the jdk would put java on my PATH, but it does not appear to work. For now, do it by hand.
31 lines
1.1 KiB
Diff
31 lines
1.1 KiB
Diff
--- fastqc.orig 2015-11-20 09:25:00.000000000 +0000
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+++ fastqc 2016-10-24 19:06:16.734000000 +0000
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@@ -38,12 +38,21 @@
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$delimiter = ';';
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}
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-if ($ENV{CLASSPATH}) {
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- $ENV{CLASSPATH} .= "$delimiter$RealBin$delimiter$RealBin/sam-1.103.jar$delimiter$RealBin/jbzip2-0.9.jar$delimiter$RealBin/cisd-jhdf5.jar";
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-}
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-else {
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- $ENV{CLASSPATH} = "$RealBin$delimiter$RealBin/sam-1.103.jar$delimiter$RealBin/jbzip2-0.9.jar$delimiter$RealBin/cisd-jhdf5.jar";
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-}
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+# The lib dir is $RealBin/../lib
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+# start with list of jars we need and prefix them with the lib dir
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+# then stick CLASSPATH onto the front (empty or otherwise...)
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+# then filter out anything that's empty (perhaps CLASSPATH...)
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+# then join all the remainings bits with the delimiter.
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+use File::Basename;
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+use File::Spec::Functions;
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+my $_lib = catfile(dirname($RealBin), 'lib');
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+$ENV{CLASSPATH} =
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+ join($delimiter,
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+ grep {$_}
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+ ($ENV{CLASSPATH},
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+ $_lib,
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+ map {"$_lib/$_"}
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+ qw(sam-1.103.jar jbzip2-0.9.jar cisd-jhdf5.jar)));
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my @java_args;
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my @files;
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