kraken: new package (#6163)

2 files changed, 89 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/jellyfish/package.py b/var/spack/repos/builtin/packages/jellyfish/package.py
new file mode 100644
index 0000000000..e6d65838a1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/jellyfish/package.py
@@ -0,0 +1,38 @@
+##############################################################################
+# 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 Jellyfish(AutotoolsPackage):
+    """JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
+       DNA."""
+
+    homepage = "http://www.cbcb.umd.edu/software/jellyfish/"
+    url      = "http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz"
+
+    version('1.1.11', 'dc994ea8b0896156500ea8c648f24846')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('python', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/kraken/package.py b/var/spack/repos/builtin/packages/kraken/package.py
new file mode 100644
index 0000000000..3994c8c138
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kraken/package.py
@@ -0,0 +1,51 @@
+##############################################################################
+# 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 glob
+import os
+
+
+class Kraken(Package):
+    """Kraken is a system for assigning taxonomic labels to short DNA
+       sequences, usually obtained through metagenomic studies."""
+
+    homepage = "https://ccb.jhu.edu/software/kraken/"
+    url      = "https://github.com/DerrickWood/kraken/archive/v1.0.tar.gz"
+
+    version('1.0', 'e790d6b09662bbd810aa34517ef66586')
+
+    depends_on('perl', type=('build', 'run'))
+    # Does NOT support JELLYFISH 2.0. Ver 1.1.11 is the last version of
+    # JELLYFISH 1.
+    depends_on('jellyfish@1.1.11', when='@1.0')
+
+    def install(self, spec, prefix):
+        installer = Executable('./install_kraken.sh')
+        installer(self.stage.source_path)
+        mkdirp(prefix.bin)
+        files = glob.iglob('*')
+        for file in files:
+            if os.path.isfile(file):
+                install(file, prefix.bin)