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| author | Luke Diorio-Toth <ldioriototh@gmail.com> | 2023-02-27 16:25:21 -0600 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2023-02-27 16:25:21 -0600 |
| commit | 779e80b7c1a75f458b4f4525be8515af76727e89 (patch) | |
| tree | 73595c328bfbd011c901b20a20f84d5cd8f9c6bb | |
| parent | 502e216ee2360a861f9db705c8246bba13a86155 (diff) | |
| download | spack-779e80b7c1a75f458b4f4525be8515af76727e89.tar.gz spack-779e80b7c1a75f458b4f4525be8515af76727e89.tar.bz2 spack-779e80b7c1a75f458b4f4525be8515af76727e89.tar.xz spack-779e80b7c1a75f458b4f4525be8515af76727e89.zip | |
Package/py pysam macos (#33851)
* cleaned up style, linked to external htslib
* removed htslib/bcfrools/samtools deps, use bundled libs instead
the pysam package includes the necessary libs to link to, so it wasn't even using linked libs when building
* fixed style
* revert to using external htslib
currently uses bundled samtools and bcftools, and there is no way to use external versions for those dependencies
* added libs property to htslibs package
added support for lib64
* added htslib name
| -rw-r--r-- | var/spack/repos/builtin/packages/htslib/package.py | 4 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/py-pysam/package.py | 15 |
2 files changed, 15 insertions, 4 deletions
diff --git a/var/spack/repos/builtin/packages/htslib/package.py b/var/spack/repos/builtin/packages/htslib/package.py index 7305661d0c..b2c5a0ac01 100644 --- a/var/spack/repos/builtin/packages/htslib/package.py +++ b/var/spack/repos/builtin/packages/htslib/package.py @@ -52,6 +52,10 @@ class Htslib(AutotoolsPackage): depends_on("automake", when="@1.2") depends_on("libtool", when="@1.2") + @property + def libs(self): + return find_libraries("libhts", root=self.prefix, recursive=True) + # v1.2 uses the automagically assembled tarball from .../archive/... # everything else uses the tarballs uploaded to the release def url_for_version(self, version): diff --git a/var/spack/repos/builtin/packages/py-pysam/package.py b/var/spack/repos/builtin/packages/py-pysam/package.py index afacbee9bf..2b98316c15 100644 --- a/var/spack/repos/builtin/packages/py-pysam/package.py +++ b/var/spack/repos/builtin/packages/py-pysam/package.py @@ -26,11 +26,18 @@ class PyPysam(PythonPackage): depends_on("py-cython@0.21:", when="@0.14:", type="build") depends_on("py-cython@0.17:", type="build") depends_on("curl") - depends_on("bcftools") - depends_on("htslib") - depends_on("samtools") - + depends_on("xz") depends_on("htslib@:1.6", when="@:0.13") + depends_on("htslib") def setup_build_environment(self, env): env.set("LDFLAGS", self.spec["curl"].libs.search_flags) + # this flag is supposed to be removed by cy_build.py, but for some reason isn't + if self.spec.platform == "darwin": + env.remove_flags("LDSHARED", "-bundle") + # linking htslib, see: + # http://pysam.readthedocs.org/en/latest/installation.html#external + # https://github.com/pysam-developers/pysam/blob/v0.9.0/setup.py#L79 + env.set("HTSLIB_MODE", "external") + env.set("HTSLIB_LIBRARY_DIR", self.spec["htslib"].libs.directories[0]) + env.set("HTSLIB_INCLUDE_DIR", self.spec["htslib"].headers.directories[0]) |