From d7c9128875f679ba72e39a3b2b8ff7f31e3bee94 Mon Sep 17 00:00:00 2001 From: Justin Stanley Date: Fri, 2 Nov 2018 20:18:05 -0500 Subject: new package: homer (starting at 4.9.1) (#9669) --- var/spack/repos/builtin/packages/homer/package.py | 48 +++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 var/spack/repos/builtin/packages/homer/package.py diff --git a/var/spack/repos/builtin/packages/homer/package.py b/var/spack/repos/builtin/packages/homer/package.py new file mode 100644 index 0000000000..14293169dc --- /dev/null +++ b/var/spack/repos/builtin/packages/homer/package.py @@ -0,0 +1,48 @@ +# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * +from os import symlink + + +class Homer(Package): + """Software for motif discovery and next generation sequencing analysis""" + + homepage = "http://homer.ucsd.edu/homer" + url = "http://homer.ucsd.edu/homer/data/software/homer.v4.9.zip" + + version('4.9.1', sha256='ad1303b0b0400dc8a88dbeae1ee03a94631977b751a3d335326c4febf0eec3a9') + + depends_on('perl', type=('build', 'run')) + depends_on('r-biocgenerics', type='run') + depends_on('r-biocparallel', type='run') + depends_on('r-edger', type='run') + depends_on('r-deseq2', type='run') + + variant('data', default=False, + description='Download genome data packages') + + def install(self, spec, prefix): + # initialize homer directories + basedir = join_path(prefix.lib, 'homer') + mkdirp(basedir) + + install_tree('.', basedir) + + # symlink bin so it is included in the PATH + symlink(join_path(basedir, 'bin'), prefix.bin) + + # override homer base directory in configure script + filter_file('my $homeDir = $1;', + 'my $homeDir = \"{0}\";'.format(basedir), + 'configureHomer.pl', string=True) + + # compile/prepare binaries and perl scripts with the correct paths + perl = which('perl') + perl('configureHomer.pl', '-local') + + # download extra data if requested + if '+data' in spec: + perl('configureHomer.pl', '-install', '-all') -- cgit v1.2.3-70-g09d2