Package for bcl2fastq2 (updates libxslt) (#4234)
* Add v1.1.26 and make crypto a variant I need 1.1.26 for bcl2fastq2. I also need to build it without crypto support. * Initial support for bcl2fastq2 * Clean up commentary, messages, names No substantial changes intended, just cleanup. * fix flake8 and extra import * The masked grammarian strikes again... * Be normal (messages don't end in periods) * When +crypto, add --with-crypto Add `--with-crypto` to configure args when user hasn't explicitly set `~crypto`. * self.spec.satisfies is unsatisfying, in is in instead See #4135, self.spec.satisfies has issues. @adamjstewart suggests simply using in.
This commit is contained in:
George Hartzell
Adam J. Stewart
parent
32c570913d
commit
daaa37c1ff
4 changed files with 131 additions and 2 deletions
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@ -0,0 +1,10 @@
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--- a/src/cmake/bcl2fastq_redist_macros.cmake 2017-05-11 15:03:27.652495488 -0700
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+++ b/src/cmake/bcl2fastq_redist_macros.cmake 2017-05-11 15:06:38.326745889 -0700
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@@ -30,6 +30,7 @@
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message(" Found: ${libname}, correct version ${version}")
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message(" ${${libname}_UPPER}_INCLUDE_DIR = ${${${libname}_UPPER}_INCLUDE_DIR}")
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message(" ${${libname}_UPPER}_LIBRARIES = ${${${libname}_UPPER}_LIBRARIES}")
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+ set (HAVE_${${libname}_UPPER} true CACHE BOOL "package" FORCE)
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else("${${${libname}_UPPER}_VERSION_STRING}" STREQUAL "${version}")
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message(" Not found: ${libname}, incorrect version ( ${${${libname}_UPPER}_VERSION} )")
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set(${${libname}_UPPER}_FOUND "FALSE")
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@ -0,0 +1,12 @@
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--- a/src/cmake/cxxConfigure.cmake 2017-05-11 16:55:14.745107845 -0700
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+++ b/src/cmake/cxxConfigure.cmake 2017-05-11 17:16:39.355981745 -0700
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@@ -101,6 +101,9 @@
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if((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT))
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find_package_version(LibXml2 ${BCL2FASTQ_LIBXML2_VERSION})
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find_package_version(LibXslt ${BCL2FASTQ_LIBXSLT_VERSION})
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+ # macro isn't ONLY for redist, see its definition...
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+ string(REGEX REPLACE "/include$" "" LIBEXSLT_HINT ${LIBXSLT_INCLUDE_DIR})
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+ find_library_redist(LIBEXSLT ${LIBEXSLT_HINT} libexslt/exslt.h exslt)
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endif((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT))
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if((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT))
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95
var/spack/repos/builtin/packages/bcl2fastq2/package.py
Normal file
95
var/spack/repos/builtin/packages/bcl2fastq2/package.py
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@ -0,0 +1,95 @@
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the LICENSE file for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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import os
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import shutil
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import llnl.util.tty as tty
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# This application uses cmake to build, but they wrap it with a
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# configure script that performs dark magic. This package does it
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# their way.
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class Bcl2fastq2(Package):
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"""The bcl2fastq2 Conversion Software converts base
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call (BCL) files from a sequencing run into FASTQ
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files."""
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homepage = "https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-18.html"
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url = "https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v2-18-0-12-tar.zip"
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version('2-18-0-12', 'fbe06492117f65609c41be0c27e3215c')
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depends_on('boost@1.54.0')
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depends_on('cmake@2.8.9:')
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depends_on('libxml2@2.7.8')
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depends_on('libxslt@1.1.26~crypto')
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depends_on('libgcrypt')
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depends_on('zlib')
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# Their cmake macros don't set the flag when they find a library
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# that makes them happy.
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patch('cmake-macros.patch')
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# After finding the libxslt bits, cmake still needs to wire in the
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# libexslt bits.
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patch('cxxConfigure-cmake.patch')
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root_cmakelists_dir = '../src'
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def url_for_version(self, version):
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url = "https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v{0}-tar.zip"
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return url.format(version.dashed)
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# Illumina tucks the source inside a gzipped tarball inside a zip
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# file. We let the normal Spack expansion bit unzip the zip file,
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# then follow it with a function untars the tarball after Spack's
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# done it's bit.
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def do_stage(self, mirror_only=False):
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# wrap (decorate) the standard expand_archive step with a
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# helper, then call the real do_stage().
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self.stage.expand_archive = self.unpack_it(self.stage.expand_archive)
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super(Bcl2fastq2, self).do_stage(mirror_only)
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def unpack_it(self, f):
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def wrap():
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f() # call the original expand_archive()
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if os.path.isdir('bcl2fastq'):
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tty.msg("The tarball has already been unpacked")
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else:
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tty.msg("Unpacking bcl2fastq2 tarball")
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tarball = 'bcl2fastq2-v{0}.tar.gz'.format(self.version.dotted)
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shutil.move(join_path('spack-expanded-archive', tarball), '.')
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os.rmdir('spack-expanded-archive')
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tar = which('tar')
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tar('-xf', tarball)
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tty.msg("Finished unpacking bcl2fastq2 tarball")
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return wrap
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def install(self, spec, prefix):
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bash = which('bash')
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bash("src/configure", "--prefix={0}".format(prefix),
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"--with-cmake={0}".format(join_path(spec['cmake'].prefix.bin,
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"cmake")))
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make()
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make("install")
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@ -36,10 +36,22 @@ class Libxslt(AutotoolsPackage):
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homepage = "http://www.xmlsoft.org/XSLT/index.html"
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url = "http://xmlsoft.org/sources/libxslt-1.1.28.tar.gz"
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version('1.1.28', '9667bf6f9310b957254fdcf6596600b7')
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version('1.1.29', 'a129d3c44c022de3b9dcf6d6f288d72e')
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version('1.1.28', '9667bf6f9310b957254fdcf6596600b7')
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version('1.1.26', 'e61d0364a30146aaa3001296f853b2b9')
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variant('crypto', default=True,
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description='Build libexslt with crypto support')
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depends_on("libxml2")
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depends_on("xz")
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depends_on("zlib")
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depends_on("libgcrypt")
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depends_on("libgcrypt", when="+crypto")
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def configure_args(self):
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args = []
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if '~crypto' in self.spec:
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args.append('--without-crypto')
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else:
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args.append('--with-crypto')
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return args
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