hisat2: new package (#5488)

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)