casper: new package (#6873)

* casper: create package

* jellyfish: added version 2.2.7

* casper: new package

* casper: depends on jellyfish 2.2.3 or higher

* casper: moved depends_on above install

* casper: updated package.py

* fixing download url for 1.11.1

* casper: set up environment

* casper: add conflicts gcc@7.1.0, cannot install with 7.1.0

* capser: flake8 error corrcted

* casper: create package

* jellyfish: added version 2.2.7

* casper: new package

* casper: depends on jellyfish 2.2.3 or higher

* casper: moved depends_on above install

* casper: updated package.py

* fixing download url for 1.11.1

* casper: set up environment

* casper: add conflicts gcc@7.1.0, cannot install with 7.1.0

* capser: flake8 error corrcted

var/spack/repos/builtin/packages/casper/package.py

+##############################################################################
+# 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 *
+import distutils.dir_util
+
+
+class Casper(MakefilePackage):
+    """CASPER (Context-Aware Scheme for Paired-End Read) is state-of-the art
+       merging tool in terms of accuracy and robustness. Using this
+       sophisticated merging method, we could get elongated reads from the
+       forward and reverse reads."""
+
+    homepage = "http://best.snu.ac.kr/casper/index.php?name=main"
+    url      = "http://best.snu.ac.kr/casper/program/casper_v0.8.2.tar.gz"
+
+    version('0.8.2', '9e83d32ff46b876f33eb1d7b545ec9c2')
+
+    depends_on('jellyfish@2.2.3:')
+    depends_on('boost')
+
+    conflicts('%gcc@7.1.0')
+
+    def install(self, spec, prefix):
+        distutils.dir_util.copy_tree(".", prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.spec.prefix)

var/spack/repos/builtin/packages/jellyfish/package.py

@@ -30,9 +30,12 @@ class Jellyfish(AutotoolsPackage):
        DNA."""
 
     homepage = "http://www.cbcb.umd.edu/software/jellyfish/"
-    url      = "http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz"
+    url      = "https://github.com/gmarcais/Jellyfish/releases/download/v2.2.7/jellyfish-2.2.7.tar.gz"
+    list_url = "http://www.cbcb.umd.edu/software/jellyfish/"
 
-    version('1.1.11', 'dc994ea8b0896156500ea8c648f24846')
+    version('2.2.7', 'f741192d9061f28e34cb67c86a1027ab')
+    version('1.1.11', 'dc994ea8b0896156500ea8c648f24846',
+            url='http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz')
 
     depends_on('perl', type=('build', 'run'))
     depends_on('python', type=('build', 'run'))