diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/scalpel/package.py | 101 |
1 files changed, 101 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/scalpel/package.py b/var/spack/repos/builtin/packages/scalpel/package.py new file mode 100644 index 0000000000..cac85ab564 --- /dev/null +++ b/var/spack/repos/builtin/packages/scalpel/package.py @@ -0,0 +1,101 @@ +############################################################################## +# Copyright (c) 2013-2017, 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 NOTICE and LICENSE files 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 * + + +class Scalpel(MakefilePackage): + """Scalpel is a software package for detecting INDELs (INsertions and + DELetions) mutations in a reference genome which has been sequenced + with next-generation sequencing technology. + """ + + homepage = "http://scalpel.sourceforge.net/index.html" + url = "https://downloads.sourceforge.net/project/scalpel/scalpel-0.5.3.tar.gz" + + version('0.5.3', '682c9f1cd6ab2cb11c6866f303c673f0') + + depends_on('cmake') + depends_on('perl@5.10.0:') + + # bamtools needs to build before the others. + parallel = False + + @run_before('install') + def filter_sbang(self): + """Run before install so that the standard Spack sbang install hook + can fix up the path to the perl|python binary. + """ + + with working_dir(self.stage.source_path): + kwargs = {'ignore_absent': True, 'backup': False, 'string': False} + + match = '^#!/usr/bin/env perl' + perl = self.spec['perl'].command + substitute = "#!{perl}".format(perl=perl) + files = ['FindDenovos.pl', 'scalpel-export', + 'scalpel-discovery', 'FindVariants.pl', + 'FindSomatic.pl'] + filter_file(match, substitute, *files, **kwargs) + + # Scalpel doesn't actually *have* an install step. The authors + # expect you to unpack the tarball, build it in the resulting + # directory, and add that directory to your PATH. The Perl + # scripts use `FindBin` to discover the directory in which they + # live and they run their own dedicated copies of {bam,sam}tools + # and etc... by explicitly naming the executables in their directory. + # + # Rather than trying to fix their code I just copied the juicy + # bits into prefix.bin. It's not normal, but.... + # + def install(self, spec, prefix): + destdir = prefix.bin # see the note above.... + + mkdirp(destdir) + + files = ['FindSomatic.pl', 'HashesIO.pm', 'MLDBM.pm', + 'scalpel-export', 'Utils.pm', 'FindDenovos.pl', + 'FindVariants.pl', 'scalpel-discovery', + 'SequenceIO.pm', 'Usage.pm'] + for f in files: + install(f, destdir) + + dirs = ['Text', 'MLDBM', 'Parallel', ] + for d in dirs: + install_tree(d, join_path(destdir, d)) + + install_tree('bamtools-2.3.0/bin', + join_path(destdir, 'bamtools-2.3.0', 'bin')) + install_tree('bamtools-2.3.0/lib', + join_path(destdir, 'bamtools-2.3.0', 'lib')) + + mkdirp(join_path(destdir, 'bcftools-1.1')) + install('bcftools-1.1/bcftools', join_path(destdir, 'bcftools-1.1')) + + mkdirp(join_path(destdir, 'Microassembler')) + install('Microassembler/Microassembler', + join_path(destdir, 'Microassembler')) + + mkdirp(join_path(destdir, 'samtools-1.1')) + install('samtools-1.1/samtools', join_path(destdir, 'samtools-1.1')) |