From 7cb276679078ba569a7f5b79a4c39dca2fc16937 Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Mon, 2 Oct 2017 12:27:06 -0500 Subject: [PATCH] hisat2: new package (#5488) --- .../repos/builtin/packages/hisat2/package.py | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 var/spack/repos/builtin/packages/hisat2/package.py diff --git a/var/spack/repos/builtin/packages/hisat2/package.py b/var/spack/repos/builtin/packages/hisat2/package.py new file mode 100644 index 0000000000..b2eedcc56c --- /dev/null +++ b/var/spack/repos/builtin/packages/hisat2/package.py @@ -0,0 +1,63 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * +import glob +import os.path + + +class Hisat2(MakefilePackage): + """HISAT2 is a fast and sensitive alignment program for mapping + next-generation sequencing reads (whole-genome, transcriptome, and + exome sequencing data) against the general human population (as well as + against a single reference genome).""" + + homepage = "http://ccb.jhu.edu/software/hisat2" + url = "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.1.0-source.zip" + + version('2.1.0', '8b566d1b7e6c5801c8ae9824ed2da3d0') + + def install(self, spec, prefix): + install_tree('doc', prefix.doc) + install_tree('example', prefix.example) + install_tree('hisatgenotype_modules', prefix.hisatgenotype_modules) + install_tree('hisatgenotype_scripts', prefix.hisatgenotype_scripts) + install_tree('scripts', prefix.scripts) + mkdirp(prefix.bin) + install('hisat2', prefix.bin) + install('hisat2-align-s', prefix.bin) + install('hisat2-align-l', prefix.bin) + install('hisat2-build', prefix.bin) + install('hisat2-build-s', prefix.bin) + install('hisat2-build-l', prefix.bin) + install('hisat2-inspect', prefix.bin) + install('hisat2-inspect-s', prefix.bin) + install('hisat2-inspect-l', prefix.bin) + files = glob.iglob('*.py') + for file in files: + if os.path.isfile(file): + install(file, prefix.bin) + + def setup_environment(self, spack_env, run_env): + run_env.prepend_path('PATH', self.spec.prefix)