1 files changed, 46 insertions, 0 deletions
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..a6dc337882
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fr-hit/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2018 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 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)