pagit: new package (#5140)

* pagit: new package

* removed unneeded env var

1 files changed, 68 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/pagit/package.py b/var/spack/repos/builtin/packages/pagit/package.py
new file mode 100644
index 0000000000..2e41d83da3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pagit/package.py
@@ -0,0 +1,68 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 *
+
+
+class Pagit(Package):
+    """PAGIT addresses the need for software to generate high quality draft
+       genomes."""
+
+    homepage = "http://www.sanger.ac.uk/science/tools/pagit"
+    url      = "ftp://ftp.sanger.ac.uk/pub/resources/software/pagit/PAGIT.V1.01.64bit.tgz"
+
+    version('1.01', '2c4e8512c8c02073146b50b328962e9d')
+
+    depends_on('java', type=('build', 'run'))
+    depends_on('perl', type=('build', 'run'))
+
+    def url_for_version(self, version):
+        url = 'ftp://ftp.sanger.ac.uk/pub/resources/software/pagit/PAGIT.V{0}.64bit.tgz'
+        return url.format(version)
+
+    def install(self, spec, prefix):
+        with working_dir('PAGIT'):
+            install_tree('ABACAS', prefix.ABACAS)
+            install_tree('bin', prefix.bin)
+            install_tree('ICORN', prefix.ICORN)
+            install_tree('IMAGE', prefix.IMAGE)
+            install_tree('lib', prefix.lib)
+            install_tree('RATT', prefix.RATT)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('PAGIT_HOME', self.prefix)
+        run_env.set('PILEUP_HOME', join_path(self.prefix.bin, 'pileup_v0.5'))
+        run_env.set('ICORN_HOME', self.prefix.icorn)
+        run_env.set('SNPOMATIC_HOME', self.prefix.bin)
+        run_env.set('RATT_HOME', self.prefix.RATT)
+        run_env.set('RATT_CONFIG', join_path(self.prefix.RATT, 'RATT_config'))
+        run_env.prepend_path('PATH', join_path(self.prefix.bin, 'pileup_v0.5',
+                             'ssaha2'))
+        run_env.prepend_path('PATH', join_path(self.prefix.bin,
+                             'pileup_v0.5'))
+        run_env.prepend_path('PATH', self.prefix.IMAGE)
+        run_env.prepend_path('PATH', self.prefix.ABACAS)
+        run_env.prepend_path('PATH', self.prefix.ICORN)
+        run_env.prepend_path('PATH', self.prefix.RATT)
+        run_env.prepend_path('PERL5LIB', self.prefix.lib)