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-rw-r--r--var/spack/repos/builtin/packages/scalpel/package.py101
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diff --git a/var/spack/repos/builtin/packages/scalpel/package.py b/var/spack/repos/builtin/packages/scalpel/package.py
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+##############################################################################
+# 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'))