Bioawk: added new package (#5375)

1 files changed, 51 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/bioawk/package.py b/var/spack/repos/builtin/packages/bioawk/package.py
new file mode 100644
index 0000000000..80d90c7149
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bioawk/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/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 *
+from shutil import copyfile
+from shutil import copymode
+
+
+class Bioawk(MakefilePackage):
+    """Bioawk is an extension to Brian Kernighan's awk, adding the support of
+       several common biological data formats, including optionally gzip'ed
+       BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.
+    """
+
+    homepage = "https://github.com/lh3/bioawk"
+    url = "https://github.com/lh3/bioawk/archive/v1.0.zip"
+
+    version('1.0', 'e423942689f944369de270900978be28')
+
+    depends_on('zlib')
+    depends_on('bison', type=('build'))
+
+    parallel = False
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        copyfile("bioawk", join_path(prefix.bin, "bioawk"))
+        copymode("bioawk", join_path(prefix.bin, "bioawk"))
+        copyfile("maketab", join_path(prefix.bin, "maketab"))
+        copymode("maketab", join_path(prefix.bin, "maketab"))