94c2e7e7b4
This PR adds 'http://' to the homepage setting of a few packages that do not have it set. Not having that set can cause problems with some wiki apps when embedding the homepage value into markdown syntax. - bowtie2 - exuberant-ctags - perl-want - samtools
84 lines
3.5 KiB
Python
84 lines
3.5 KiB
Python
# Copyright 2013-2020 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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from glob import glob
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class Bowtie2(Package):
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"""Bowtie 2 is an ultrafast and memory-efficient tool for aligning
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sequencing reads to long reference sequences"""
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homepage = "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml"
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url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.1/bowtie2-2.3.1-source.zip"
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version('2.3.5.1', sha256='335c8dafb1487a4a9228ef922fbce4fffba3ce8bc211e2d7085aac092155a53f')
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version('2.3.5', sha256='2b6b2c46fbb5565ba6206b47d07ece8754b295714522149d92acebefef08347b')
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version('2.3.4.1', sha256='a1efef603b91ecc11cfdb822087ae00ecf2dd922e03c85eea1ed7f8230c119dc')
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version('2.3.1', sha256='33bd54f5041a31878e7e450cdcf0afba08345fa1133ce8ac6fd00bf7e521a443')
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version('2.3.0', sha256='f9f841e780e78b1ae24b17981e2469e6d5add90ec22ef563af23ae2dd5ca003c')
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version('2.2.5', sha256='e22766dd9421c10e82a3e207ee1f0eb924c025b909ad5fffa36633cd7978d3b0')
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depends_on('tbb', when='@2.3.0:')
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depends_on('readline', when='@2.3.1:')
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depends_on('perl', type='run')
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depends_on('python', type='run')
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depends_on('zlib', when='@2.3.1:')
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patch('bowtie2-2.2.5.patch', when='@2.2.5', level=0)
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patch('bowtie2-2.3.1.patch', when='@2.3.1', level=0)
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patch('bowtie2-2.3.0.patch', when='@2.3.0', level=0)
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resource(name='simde', git="https://github.com/nemequ/simde",
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destination='.', when='target=aarch64:')
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# seems to have trouble with 6's -std=gnu++14
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conflicts('%gcc@6:', when='@:2.3.1')
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conflicts('@:2.3.5.0', when='target=aarch64:')
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def patch(self):
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if self.spec.target.family == 'aarch64':
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copy_tree('simde', 'third_party/simde')
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if self.spec.satisfies('%gcc@:4.8.9'):
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filter_file('-fopenmp-simd', '', 'Makefile')
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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 = ['bowtie2', ]
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filter_file(match, substitute, *files, **kwargs)
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match = '^#!/usr/bin/env python'
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python = self.spec['python'].command
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substitute = "#!{python}".format(python=python)
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files = ['bowtie2-build', 'bowtie2-inspect']
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filter_file(match, substitute, *files, **kwargs)
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def install(self, spec, prefix):
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make_arg = []
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if self.spec.target.family == 'aarch64':
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make_arg.append('POPCNT_CAPABILITY=0')
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make(*make_arg)
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mkdirp(prefix.bin)
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for bow in glob("bowtie2*"):
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install(bow, prefix.bin)
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# install('bowtie2',prefix.bin)
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# install('bowtie2-align-l',prefix.bin)
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# install('bowtie2-align-s',prefix.bin)
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# install('bowtie2-build',prefix.bin)
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# install('bowtie2-build-l',prefix.bin)
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# install('bowtie2-build-s',prefix.bin)
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# install('bowtie2-inspect',prefix.bin)
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# install('bowtie2-inspect-l',prefix.bin)
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# install('bowtie2-inspect-s',prefix.bin)
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