transabyss: new package (#4892)

* transabyss: new package and dependencies

* fixed build deps in igraph and version conflict spec in abyss

* fixed versioning stuff and package structure

*  fixed dep type

* fixing dep type for real this time

4 files changed, 123 insertions, 2 deletions

diff --git a/var/spack/repos/builtin/packages/abyss/package.py b/var/spack/repos/builtin/packages/abyss/package.py
index e8e0fb4d45..f3a9f27748 100644
--- a/var/spack/repos/builtin/packages/abyss/package.py
+++ b/var/spack/repos/builtin/packages/abyss/package.py
@@ -31,12 +31,14 @@ class Abyss(AutotoolsPackage):
        is useful for assembling genomes up to 100 Mbases in size."""
 
     homepage = "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
-    url      = "http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.0.2/abyss-2.0.2.tar.gz"
+    url      = "https://github.com/bcgsc/abyss/archive/2.0.2.tar.gz"
 
     version('2.0.2', '1623f55ad7f4586e80f6e74b1f27c798')
+    version('1.5.2', '10d6d72d1a915e618d41a5cbbcf2364c')
 
     depends_on('mpi')
-    depends_on('boost@:1.50.0,1.53.0:')
+    depends_on('boost@:1.50.0,1.53.0:', when='@2.0.2:')
+    depends_on('boost@:1.50.0,1.53.0:1.59.0', when='@:1.5.2')
     depends_on('sparsehash')
     depends_on('sqlite')
 
diff --git a/var/spack/repos/builtin/packages/igraph/package.py b/var/spack/repos/builtin/packages/igraph/package.py
new file mode 100644
index 0000000000..030ef1f604
--- /dev/null
+++ b/var/spack/repos/builtin/packages/igraph/package.py
@@ -0,0 +1,36 @@
+##############################################################################
+# 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 Igraph(AutotoolsPackage):
+    """igraph is a library for creating and manipulating graphs."""
+
+    homepage = "http://igraph.org/"
+    url      = "https://github.com/igraph/igraph/releases/download/0.7.1/igraph-0.7.1.tar.gz"
+
+    version('0.7.1', '4f6e7c16b45fce8ed423516a9786e4e8')
+
+    depends_on('libxml2')
diff --git a/var/spack/repos/builtin/packages/py-igraph/package.py b/var/spack/repos/builtin/packages/py-igraph/package.py
new file mode 100644
index 0000000000..7d9c408678
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-igraph/package.py
@@ -0,0 +1,38 @@
+##############################################################################
+# 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 PyIgraph(PythonPackage):
+    """igraph is a collection of network analysis tools with the emphasis on
+       efficiency, portability and ease of use."""
+
+    homepage = "http://igraph.org/"
+    url      = "http://igraph.org/nightly/get/python/python-igraph-0.7.0.tar.gz"
+
+    version('0.7.0', '32a3238cb9041b1686d7d0ba152235bf')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('igraph')
diff --git a/var/spack/repos/builtin/packages/transabyss/package.py b/var/spack/repos/builtin/packages/transabyss/package.py
new file mode 100644
index 0000000000..10ee508899
--- /dev/null
+++ b/var/spack/repos/builtin/packages/transabyss/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# 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 Transabyss(Package):
+    """De novo assembly of RNAseq data using ABySS"""
+
+    homepage = "http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss"
+    url      = "http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/releases/1.5.5/transabyss-1.5.5.zip"
+
+    version('1.5.5', '9ebe0394243006f167135cac4df9bee6')
+
+    depends_on('abyss@1.5.2')
+    depends_on('python@2.7.6:', type=('build', 'run'))
+    depends_on('py-igraph@0.7.0:', type=('build', 'run'))
+    depends_on('blat')
+
+    def install(self, spec, prefix):
+        install('transabyss', prefix)
+        install('transabyss-merge', prefix)
+        install_tree('bin', prefix.bin)
+        install_tree('utilities', prefix.utilities)