From 757528d5fbf6fa098e8eb558a4716a5be24a809d Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Tue, 13 Apr 2021 17:02:21 -0500 Subject: genemark-et package: add version 4.65 and new dependencies (#22966) New version has new dependencies (which are also added here as new packages): * perl-mce * perl-threads * perl-thread-queue The new version of genemark-et also has a different URL scheme. --- .../repos/builtin/packages/genemark-et/package.py | 11 +++++++++-- .../repos/builtin/packages/perl-mce/package.py | 22 ++++++++++++++++++++++ .../builtin/packages/perl-thread-queue/package.py | 18 ++++++++++++++++++ .../repos/builtin/packages/perl-threads/package.py | 15 +++++++++++++++ 4 files changed, 64 insertions(+), 2 deletions(-) create mode 100644 var/spack/repos/builtin/packages/perl-mce/package.py create mode 100644 var/spack/repos/builtin/packages/perl-thread-queue/package.py create mode 100644 var/spack/repos/builtin/packages/perl-threads/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/genemark-et/package.py b/var/spack/repos/builtin/packages/genemark-et/package.py index 40960be5af..962b557ffb 100644 --- a/var/spack/repos/builtin/packages/genemark-et/package.py +++ b/var/spack/repos/builtin/packages/genemark-et/package.py @@ -20,17 +20,24 @@ class GenemarkEt(Package): homepage = "http://topaz.gatech.edu/GeneMark" manual_download = True + version('4.65', sha256='62ea2dfa1954ab25edcc118dbeaeacf15924274fb9ed47bc54716cfd15ad04fe') version('4.46', sha256='856b0b6c7cbd12835e140ff04ecd9124376348efd65f76bfd8b8e08c1834eac0') version('4.38', sha256='cee3bd73d331be44159eac15469560d0b07ffa2c98ac764c37219e1f3b7d3146') depends_on('perl', type=('build', 'run')) depends_on('perl-yaml', type=('build', 'run')) depends_on('perl-hash-merge', type=('build', 'run')) - depends_on('perl-logger-simple', type=('build', 'run')) depends_on('perl-parallel-forkmanager', type=('build', 'run')) + depends_on('perl-logger-simple', when='@:4.46', type=('build', 'run')) + depends_on('perl-mce', when='@4.65:', type=('build', 'run')) + depends_on('perl-thread-queue', when='@4.65:', type=('build', 'run')) + depends_on('perl-threads', when='@4.65:', type=('build', 'run')) def url_for_version(self, version): - return "file://{0}/gm_et_linux_64.tar.gz".format(os.getcwd()) + if version >= Version('4.65'): + return "file://{0}/gmes_linux_64.tar.gz".format(os.getcwd()) + else: + return "file://{0}/gm_et_linux_64.tar.gz".format(os.getcwd()) def install(self, spec, prefix): mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/perl-mce/package.py b/var/spack/repos/builtin/packages/perl-mce/package.py new file mode 100644 index 0000000000..4281e375cd --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-mce/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2021 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 PerlMce(PerlPackage): + """MCE - Many-Core Engine for Perl providing parallel processing + capabilities. + + MCE spawns a pool of workers and therefore does not fork a new process per + each element of data. Instead, MCE follows a bank queuing model. Imagine + the line being the data and bank-tellers the parallel workers. MCE enhances + that model by adding the ability to chunk the next n elements from the + input stream to the next available worker.""" + + homepage = "https://github.com/marioroy/mce-perl" + url = "https://cpan.metacpan.org/authors/id/M/MA/MARIOROY/MCE-1.874.tar.gz" + + version('1.874', sha256='d809e3018475115ad7eccb8bef49bde3bf3e75abbbcd80564728bbcfab86d3d0') diff --git a/var/spack/repos/builtin/packages/perl-thread-queue/package.py b/var/spack/repos/builtin/packages/perl-thread-queue/package.py new file mode 100644 index 0000000000..05d5faa44b --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-thread-queue/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2021 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 PerlThreadQueue(PerlPackage): + """Thread::Queue - Thread-safe queues. + + This module provides thread-safe FIFO queues that can be accessed safely by + any number of threads.""" + + homepage = "https://metacpan.org/pod/Thread::Queue" + url = "https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN/Thread-Queue-3.13.tar.gz" + + version('3.13', sha256='6ba3dacddd2fbb66822b4aa1d11a0a5273cd04c825cb3ff31c20d7037cbfdce8') diff --git a/var/spack/repos/builtin/packages/perl-threads/package.py b/var/spack/repos/builtin/packages/perl-threads/package.py new file mode 100644 index 0000000000..52253feb5b --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-threads/package.py @@ -0,0 +1,15 @@ +# Copyright 2013-2021 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 PerlThreads(PerlPackage): + """threads - Perl interpreter-based threads""" + + homepage = "https://metacpan.org/pod/threads" + url = "https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN/threads-2.21.tar.gz" + + version('2.21', sha256='28394c98a2bcae6f20ffb8a3d965a1c194b764c650169e2050ee38dbaa10f110') -- cgit v1.2.3-70-g09d2