62927654dd
We'd like to use a consistent checksum scheme everywhere so that we can:
a) incorporate archive checksums into our specs and have a
consistent hashing algorithm across all specs.
b) index mirrors with a consistent type of checksum, and not one that
is dependent on how spack packages are written.
- [x] convert existing md5, sha224, sha512, sha1 checksums to sha256
82 lines
3.1 KiB
Python
82 lines
3.1 KiB
Python
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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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', sha256='d45b569fe3aa5934883bc7216c243d53168351c23e020d96a46fa77a1563b65e')
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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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