fr-hit: Create new package (#7132)

2 files changed, 72 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/fr-hit/binning.patch b/var/spack/repos/builtin/packages/fr-hit/binning.patch
new file mode 100644
index 0000000000..4ee81d5d83
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fr-hit/binning.patch
@@ -0,0 +1,7 @@
+--- a/binning-1.1.1/binning.py	2018-01-30 10:46:27.302198293 -0600
++++ b/binning-1.1.1/binning.py	2018-01-30 10:50:58.482866704 -0600
+@@ -1,3 +1,4 @@
++#!/usr/bin/env python
+ ######################################################
+ #      Taxonamy binning using FR-HIT output          #
+ ######################################################
diff --git a/var/spack/repos/builtin/packages/fr-hit/package.py b/var/spack/repos/builtin/packages/fr-hit/package.py
new file mode 100644
index 0000000000..03974a9642
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fr-hit/package.py
@@ -0,0 +1,65 @@
+##############################################################################
+# 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/spack/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 *
+
+
+class FrHit(Package):
+    """An efficient algorithm for fragment recruitment for next generation
+    sequences against microbial reference genomes."""
+
+    homepage = "http://weizhong-lab.ucsd.edu/frhit"
+    url      = "http://weizhong-lab.ucsd.edu/frhit/fr-hit-v0.7.1-2013-02-20.tar.gz"
+
+    version('0.7.1-2013-02-20', '3e8ea41ba09ab0c13e9973fe6f493f96')
+
+    depends_on('perl')
+    depends_on('python@2.7:')
+
+    # The patch adds the python interpreter to the beginning of the script
+    # allowing it to be run directly without passing the entire path to the
+    # script to python.
+    patch('binning.patch')
+
+    def install(self, spec, prefix):
+        make()
+
+        filter_file(
+            r'#!/bin/env perl',
+            '#!/usr/bin/env perl',
+            'frhit2pairend.pl'
+        )
+        filter_file(
+            r'#!/bin/env perl',
+            '#!/usr/bin/env perl',
+            'psl2sam.pl'
+        )
+
+        mkdirp(prefix.bin)
+        install('fr-hit', prefix.bin)
+        install('frhit2pairend.pl', prefix.bin)
+        install('psl2sam.pl', prefix.bin)
+        install('binning-1.1.1/bacteria_gitax.pkl', prefix.bin)
+        install('binning-1.1.1/binning.py', prefix.bin)
+        install('binning-1.1.1/tax.pkl', prefix.bin)