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| author | Barry Britt <barry.britt@gmail.com> | 2017-05-06 12:05:12 -0500 |
|---|---|---|
| committer | Adam J. Stewart <ajstewart426@gmail.com> | 2017-05-06 12:05:12 -0500 |
| commit | c0a52cc59e65c48d095036a43c7e574aa088d0b3 (patch) | |
| tree | c22c5f33220ce8a57ea16db2ac9f9f4824be5bcf | |
| parent | 741e4df233482bedefc000387625663cf201c231 (diff) | |
| download | spack-c0a52cc59e65c48d095036a43c7e574aa088d0b3.tar.gz spack-c0a52cc59e65c48d095036a43c7e574aa088d0b3.tar.bz2 spack-c0a52cc59e65c48d095036a43c7e574aa088d0b3.tar.xz spack-c0a52cc59e65c48d095036a43c7e574aa088d0b3.zip | |
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.
| -rw-r--r-- | var/spack/repos/builtin/packages/bamtools/package.py | 17 |
1 files changed, 9 insertions, 8 deletions
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 |