path: root/var/spack/repos/builtin/packages/bowtie2/package.py

# Copyright 2013-2020 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)


class Bowtie2(MakefilePackage):
    """Bowtie 2 is an ultrafast and memory-efficient tool for aligning
       sequencing reads to long reference sequences"""

    homepage = "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml"
    url      = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.1/bowtie2-2.3.1-source.zip"

    version('2.4.2', sha256='4cc555eeeeb8ae2d47aaa1551f3f01b57f567a013e4e0d1f30e90f462865027e')
    version('2.4.1', sha256='566d6fb01a361883747103d797308ee4bdb70f6db7d27bfc72a520587815df22')
    version('2.3.5.1', sha256='335c8dafb1487a4a9228ef922fbce4fffba3ce8bc211e2d7085aac092155a53f')
    version('2.3.5', sha256='2b6b2c46fbb5565ba6206b47d07ece8754b295714522149d92acebefef08347b')
    version('2.3.4.1', sha256='a1efef603b91ecc11cfdb822087ae00ecf2dd922e03c85eea1ed7f8230c119dc')
    version('2.3.1', sha256='33bd54f5041a31878e7e450cdcf0afba08345fa1133ce8ac6fd00bf7e521a443')
    version('2.3.0', sha256='f9f841e780e78b1ae24b17981e2469e6d5add90ec22ef563af23ae2dd5ca003c')
    version('2.2.5', sha256='e22766dd9421c10e82a3e207ee1f0eb924c025b909ad5fffa36633cd7978d3b0')

    depends_on('tbb', when='@2.3.0:')
    depends_on('readline', when='@2.3.1:')
    depends_on('perl', type='run')
    depends_on('python', type='run')
    depends_on('zlib', when='@2.3.1:')
    depends_on('simde', type='link')

    patch('bowtie2-2.2.5.patch', when='@2.2.5', level=0)
    patch('bowtie2-2.3.1.patch', when='@2.3.1', level=0)
    patch('bowtie2-2.3.0.patch', when='@2.3.0', level=0)

    # seems to have trouble with 6's -std=gnu++14
    conflicts('%gcc@6:', when='@:2.3.1')
    conflicts('@:2.3.5.0', when='target=aarch64:')
    conflicts('@2.4.1', when='target=aarch64:')

    def edit(self, spec, prefix):
        kwargs = {'ignore_absent': True, 'backup': False, 'string': False}

        match = '^#!/usr/bin/env perl'
        perl = spec['perl'].command
        substitute = "#!{perl}".format(perl=perl)
        files = ['bowtie2', ]
        filter_file(match, substitute, *files, **kwargs)

        match = '^#!/usr/bin/env python'
        python = spec['python'].command
        substitute = "#!{python}".format(python=python)
        files = ['bowtie2-build', 'bowtie2-inspect']
        filter_file(match, substitute, *files, **kwargs)

        match = '-Ithird_party/simde'
        simdepath = spec['simde'].prefix.include
        substitute = "-I{simdepath}".format(simdepath=simdepath)
        files = ['Makefile']
        filter_file(match, substitute, *files, **kwargs)

    @property
    def build_targets(self):
        make_arg = ['PREFIX={0}'.format(self.prefix)]
        if self.spec.satisfies('target=aarch64:'):
            make_arg.append('POPCNT_CAPABILITY=0')
        return make_arg

    @property
    def install_targets(self):
        return ['PREFIX={0}'.format(self.prefix), 'install']