102 lines
4.1 KiB
Python
102 lines
4.1 KiB
Python
##############################################################################
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# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/spack/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class Scalpel(MakefilePackage):
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"""Scalpel is a software package for detecting INDELs (INsertions and
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DELetions) mutations in a reference genome which has been sequenced
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with next-generation sequencing technology.
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"""
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homepage = "http://scalpel.sourceforge.net/index.html"
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url = "https://downloads.sourceforge.net/project/scalpel/scalpel-0.5.3.tar.gz"
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version('0.5.3', '682c9f1cd6ab2cb11c6866f303c673f0')
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depends_on('cmake')
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depends_on('perl@5.10.0:')
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# bamtools needs to build before the others.
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parallel = False
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@run_before('install')
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def filter_sbang(self):
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"""Run before install so that the standard Spack sbang install hook
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can fix up the path to the perl|python binary.
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"""
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with working_dir(self.stage.source_path):
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kwargs = {'ignore_absent': True, 'backup': False, 'string': False}
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match = '^#!/usr/bin/env perl'
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perl = self.spec['perl'].command
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substitute = "#!{perl}".format(perl=perl)
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files = ['FindDenovos.pl', 'scalpel-export',
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'scalpel-discovery', 'FindVariants.pl',
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'FindSomatic.pl']
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filter_file(match, substitute, *files, **kwargs)
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# Scalpel doesn't actually *have* an install step. The authors
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# expect you to unpack the tarball, build it in the resulting
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# directory, and add that directory to your PATH. The Perl
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# scripts use `FindBin` to discover the directory in which they
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# live and they run their own dedicated copies of {bam,sam}tools
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# and etc... by explicitly naming the executables in their directory.
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#
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# Rather than trying to fix their code I just copied the juicy
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# bits into prefix.bin. It's not normal, but....
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#
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def install(self, spec, prefix):
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destdir = prefix.bin # see the note above....
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mkdirp(destdir)
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files = ['FindSomatic.pl', 'HashesIO.pm', 'MLDBM.pm',
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'scalpel-export', 'Utils.pm', 'FindDenovos.pl',
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'FindVariants.pl', 'scalpel-discovery',
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'SequenceIO.pm', 'Usage.pm']
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for f in files:
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install(f, destdir)
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dirs = ['Text', 'MLDBM', 'Parallel', ]
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for d in dirs:
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install_tree(d, join_path(destdir, d))
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install_tree('bamtools-2.3.0/bin',
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join_path(destdir, 'bamtools-2.3.0', 'bin'))
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install_tree('bamtools-2.3.0/lib',
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join_path(destdir, 'bamtools-2.3.0', 'lib'))
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mkdirp(join_path(destdir, 'bcftools-1.1'))
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install('bcftools-1.1/bcftools', join_path(destdir, 'bcftools-1.1'))
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mkdirp(join_path(destdir, 'Microassembler'))
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install('Microassembler/Microassembler',
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join_path(destdir, 'Microassembler'))
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mkdirp(join_path(destdir, 'samtools-1.1'))
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install('samtools-1.1/samtools', join_path(destdir, 'samtools-1.1'))
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