diff options
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/sambamba/Makefile.patch | 11 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/sambamba/package.py | 52 |
2 files changed, 63 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/sambamba/Makefile.patch b/var/spack/repos/builtin/packages/sambamba/Makefile.patch new file mode 100644 index 0000000000..086a137569 --- /dev/null +++ b/var/spack/repos/builtin/packages/sambamba/Makefile.patch @@ -0,0 +1,11 @@ +--- sambamba/Makefile.orig 2017-09-07 14:31:28.563896131 -0700 ++++ sambamba/Makefile 2017-09-07 14:31:35.337912872 -0700 +@@ -20,7 +20,7 @@ + + else + +-LINK_CMD=gcc -Wl,--gc-sections -o build/sambamba build/sambamba.o $(STATIC_LIB_SUBCMD) -l:libphobos2-ldc.a -l:libdruntime-ldc.a -lrt -lpthread -lm ++LINK_CMD=gcc -Wl,--gc-sections -o build/sambamba build/sambamba.o $(STATIC_LIB_SUBCMD) -l:libphobos2-ldc.a -l:libdruntime-ldc.a -lrt -lpthread -lm -ldl + DMD_STATIC_LIBS=-L-Lhtslib -L-l:libhts.a -L-l:libphobos2.a -L-Llz4/lib -L-l:liblz4.a + + define split-debug diff --git a/var/spack/repos/builtin/packages/sambamba/package.py b/var/spack/repos/builtin/packages/sambamba/package.py new file mode 100644 index 0000000000..3bd18d6e98 --- /dev/null +++ b/var/spack/repos/builtin/packages/sambamba/package.py @@ -0,0 +1,52 @@ +############################################################################## +# 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 * + + +class Sambamba(Package): + """Sambamba: process your BAM data faster (bioinformatics)""" + + homepage = "http://lomereiter.github.io/sambamba/" + + version('0.6.6', git='https://github.com/lomereiter/sambamba.git', + tag='v0.6.6', submodules=True) + + depends_on('ldc~shared', type=('build', 'link')) + depends_on('python', type='build') + + resource( + name='undeaD', + git='https://github.com/dlang/undeaD.git', + tag='v1.0.7', + ) + + patch('Makefile.patch') + parallel = False + + def install(self, spec, prefix): + make('sambamba-ldmd2-64') + mkdirp(prefix.bin) + for filename in ('build/sambamba', 'build/sambamba.debug'): + install(filename, prefix.bin) |