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# Copyright 2013-2019 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 *
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('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'))
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