diff options
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/fastqc/fastqc.patch | 30 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/fastqc/package.py | 60 |
2 files changed, 90 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/fastqc/fastqc.patch b/var/spack/repos/builtin/packages/fastqc/fastqc.patch new file mode 100644 index 0000000000..a0a1155905 --- /dev/null +++ b/var/spack/repos/builtin/packages/fastqc/fastqc.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; diff --git a/var/spack/repos/builtin/packages/fastqc/package.py b/var/spack/repos/builtin/packages/fastqc/package.py new file mode 100644 index 0000000000..e2a1b54210 --- /dev/null +++ b/var/spack/repos/builtin/packages/fastqc/package.py @@ -0,0 +1,60 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * +from distutils.dir_util import copy_tree, mkpath +from distutils.file_util import copy_file + + +class Fastqc(Package): + """A quality control tool for high throughput sequence data.""" + + homepage = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" + url = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip" + + version('0.11.5', '3524f101c0ab0bae77c7595983170a76') + + depends_on('jdk', type='run') + depends_on('perl') # for fastqc "script", any perl will do + + patch('fastqc.patch', level=0) + + def install(self, spec, prefix): + mkpath(self.prefix.bin) + mkpath(self.prefix.lib) + copy_file('fastqc', self.prefix.bin) + for j in ['cisd-jhdf5.jar', 'jbzip2-0.9.jar', 'sam-1.103.jar']: + copy_file(j, self.prefix.lib) + for d in ['Configuration', 'net', 'org', 'Templates', 'uk']: + copy_tree(d, join_path(self.prefix.lib, d)) + chmod = which('chmod') + chmod('+x', join_path(self.prefix.bin, 'fastqc')) + + # In theory the 'run' dependency on 'jdk' above should take + # care of this for me. In practice, it does not. + def setup_environment(self, spack_env, env): + """Add <prefix> to the path; the package has a script at the + top level. + """ + env.prepend_path('PATH', join_path(self.spec['jdk'].prefix, 'bin')) |