From c0a52cc59e65c48d095036a43c7e574aa088d0b3 Mon Sep 17 00:00:00 2001 From: Barry Britt Date: Sat, 6 May 2017 12:05:12 -0500 Subject: Updating bamtools to include a dependency for zlib. (#4031) * Updating bamtools to include a dependency for zlib. In a standard compile, bamtools will fail if zlib headers are not installed on the target machine. In order to maintain compatibility with all systems -- and since zlib is included already as a dependency for cmake -- this patch adds zlib as a link dependency for the bamtools package. * Modified cmake rpath include. Bamtools has a non-standard library location, so we need to append $prefix/lib/bamtools to the rpath. Not sure there's a better way to do this... * Fixing syntax error in package.py Fixed a non-terminated parenthesis on line 46. * Updated bamtools to be a CMakePackage Removed extraneous code, and altered the package to extend cmake_args including the non-standard library location. * UpRemoving cmake dependency and removing blank line from end of file * Updates to cmake_args. Removed the duplicate definition of std_cmake_args in favor of simply overriding the CMAKE_INSTALL_RPATH variable that is provided. This should allow the package to be linked correctly to itself. --- var/spack/repos/builtin/packages/bamtools/package.py | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/bamtools/package.py b/var/spack/repos/builtin/packages/bamtools/package.py index 6ad90c779b..79e71cc0f2 100644 --- a/var/spack/repos/builtin/packages/bamtools/package.py +++ b/var/spack/repos/builtin/packages/bamtools/package.py @@ -23,9 +23,10 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * +import os -class Bamtools(Package): +class Bamtools(CMakePackage): """C++ API & command-line toolkit for working with BAM data.""" homepage = "https://github.com/pezmaster31/bamtools" @@ -36,11 +37,11 @@ class Bamtools(Package): version('2.3.0', 'd327df4ba037d6eb8beef65d7da75ebc') version('2.2.3', '6eccd3e45e4ba12a68daa3298998e76d') - depends_on('cmake', type='build') + depends_on('zlib', type='link') - def install(self, spec, prefix): - with working_dir('spack-build', create=True): - cmake('..', *std_cmake_args) - - make() - make('install') + def cmake_args(self): + args = [] + rpath = self.rpath + rpath.append(os.path.join(self.prefix.lib, "bamtools")) + args.append("-DCMAKE_INSTALL_RPATH=%s" % ':'.join(rpath)) + return args -- cgit v1.2.3-70-g09d2