reinit the tree, so we can have metadata

4 files changed, 128 insertions, 0 deletions

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
new file mode 100644
index 000000000000..98f7f4b6eb34
--- /dev/null
+++ b/sci-biology/pysam/Manifest
@@ -0,0 +1,6 @@
+AUX pysam-0.12-fix-buildsystem.patch 2356 SHA256 973ab655536c8d0d8e815d1a227655aeb1389d77b488bcc0a40f1cd20faed67a SHA512 24c5c521ddd2e8a88a713c2cab2aedb0cd9a589e2ae87696a60815f9714e2b222a5e0824c5ac293f9023f6f772a599256a5c07228b5a2df40b62a1bf7616c84a WHIRLPOOL 7648f5fb4c2db008a2c667f12f366dfff8e8f46127580980f893da7face03dbcbe7d70c1ca8cf8595e086d7db4acd8b6339eb51ac124bfd03cba3e60ca5101c4
+DIST pysam-0.12.0.1.tar.gz 2672020 SHA256 04837bf0b1313e57d50076f228463262b9982c410b973eb184c033528f83d523 SHA512 31460ca98ad2ac5489905ffce76bfbb5bf4a295159f3cc8e088c78dcfbfc34b30d6f7871fd1454de01da98f82b7438ac2aca678a771d7b97ae0029a418f29f1d WHIRLPOOL 5bd9f29e7458cac3839aaa9703d4c5740b1268644947f31ce7d3ddd12e0ec1948611ca5228323ce9b3b8fa5a5e0623c6fa0a0e2ce7f197fdb81aa5465915af36
+EBUILD pysam-0.12.0.1.ebuild 1204 SHA256 6e6adf1e8d4641fd59a98212b62885b05a35e7851f6773952e9b21853cb69975 SHA512 cca0548e77c3c3cd10f6253cdafb7be9c2ae094490aa9dd019b7b09e5cd0f273e9a350275a35eb55d6ddce4e46cc549f7b462f5fd4b06cfa012f1344263d41a7 WHIRLPOOL 50b3df57a0617b32e1c41fe46581ca867278f675a08ce78565be45b7d6ed5f94a902075b2dc9a7eb0307f340da5e319f88c2a69e72a588339a4d8f7d3cc490e5
+MISC ChangeLog 3211 SHA256 814821b212b72f1e2a855be2286756b938d2f77e77699c0c74a6780e9bc139ed SHA512 a2d8aea3e52e94118ba0474fc1188fb2456693a610a2ce4654ceff67fea53748df8745d5b038439abf5424f085f65314721225f0cfb65b26535ae88ddf988060 WHIRLPOOL 6630495ece6d70293fde494ce8cac7411687353f32f1b0012ad5eddea4e50eb6559ec748d4c339561327119217771a8de6ec5f108ebaff9442752b4ce2927ec2
+MISC ChangeLog-2015 858 SHA256 1aebf8e09643d1ee9a87f229d0b8813617a053ce373e3e394463b9914bdc84e9 SHA512 8ad50a8a9a15a83cec9c562b3f23b1b54c15aa2c0fb0c0757fe8b6471ac4dcb17d3cc5f98d3a669def5c3882b0943358280cf1d2ef75054f558d438787d37b62 WHIRLPOOL dd094a7d3b5f6cef469f36980243a9b3c033ca39c2f89052cb67c2c46395325a78f4e8968fa449d5b48b4fc6a8d976645cddf3d313e7d499011afddb57ae3703
+MISC metadata.xml 410 SHA256 a683ef3244d84e185203d717ab774d02fbc0dad51f7b95149b3dcf6fba0347c8 SHA512 38bcd511561b2466ef5d39473a6d1a838af0aff6eeb520307331fe0fc3177be3062fa0be39f48a333bb8e31841115cafd9dfb80a5985c316c9b8df1609f00810 WHIRLPOOL 0d34249bc0ce40ce5ede763e5ff599b2de67a6d07977da6ae3498d9d35be854673e02f69d3c20449998ce169d3cf3da76472c8ed0b5ef6d16a7de3110d536c01
diff --git a/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch b/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch
new file mode 100644
index 000000000000..8b323a63fba5
--- /dev/null
+++ b/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch
@@ -0,0 +1,63 @@
+The build system is not designed with partial out-of-source
+builds in mind. This is evident by using relative includes
+such as '-Isamtools' instead of proper relative or absolute
+paths.
+
+Bug: https://bugs.gentoo.org/show_bug.cgi?id=629670
+
+--- a/setup.py
++++ b/setup.py
+@@ -359,6 +359,8 @@
+ 
+ define_macros = []
+ 
++samtools_include_dirs = [os.path.abspath("samtools")]
++
+ chtslib = Extension(
+     "pysam.libchtslib",
+     [source_pattern % "htslib",
+@@ -385,7 +387,7 @@
+     htslib_sources +
+     os_c_files,
+     library_dirs=htslib_library_dirs,
+-    include_dirs=["pysam", "samtools", "."] + include_os + htslib_include_dirs,
++    include_dirs=["pysam", "."] + samtools_include_dirs + include_os + htslib_include_dirs,
+     libraries=external_htslib_libraries + internal_htslib_libraries,
+     language="c",
+     extra_compile_args=extra_compile_args,
+@@ -404,7 +406,7 @@
+     htslib_sources +
+     os_c_files,
+     library_dirs=htslib_library_dirs,
+-    include_dirs=["pysam", "samtools"] + include_os + htslib_include_dirs,
++    include_dirs=["pysam"] + samtools_include_dirs + include_os + htslib_include_dirs,
+     libraries=external_htslib_libraries + internal_htslib_libraries,
+     language="c",
+     extra_compile_args=extra_compile_args,
+@@ -423,7 +425,7 @@
+     htslib_sources +
+     os_c_files,
+     library_dirs=htslib_library_dirs,
+-    include_dirs=["pysam", "samtools", "."] + include_os + htslib_include_dirs,
++    include_dirs=["pysam", "."] + samtools_include_dirs + include_os + htslib_include_dirs,
+     libraries=external_htslib_libraries + internal_htslib_libraries,
+     language="c",
+     extra_compile_args=extra_compile_args,
+@@ -467,7 +469,7 @@
+     htslib_sources +
+     os_c_files,
+     library_dirs=["pysam"] + htslib_library_dirs,
+-    include_dirs=["samtools", "pysam", "."] +
++    include_dirs=["pysam", "."] + samtools_include_dirs +
+     include_os + htslib_include_dirs,
+     libraries=external_htslib_libraries + internal_htslib_libraries,
+     language="c",
+@@ -482,7 +484,7 @@
+     htslib_sources +
+     os_c_files,
+     library_dirs=["pysam"] + htslib_library_dirs,
+-    include_dirs=["bcftools", "pysam", "."] +
++    include_dirs=["bcftools", "pysam", "."] + samtools_include_dirs +
+     include_os + htslib_include_dirs,
+     libraries=external_htslib_libraries + internal_htslib_libraries,
+     language="c",
diff --git a/sci-biology/pysam/metadata.xml b/sci-biology/pysam/metadata.xml
new file mode 100644
index 000000000000..6182254bd46d
--- /dev/null
+++ b/sci-biology/pysam/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="google-code">pysam</remote-id>
+    <remote-id type="github">pysam-developers/pysam</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-biology/pysam/pysam-0.12.0.1.ebuild b/sci-biology/pysam/pysam-0.12.0.1.ebuild
new file mode 100644
index 000000000000..1f4f58fdfe29
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.12.0.1.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
+
+inherit distutils-r1
+
+DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
+HOMEPAGE="
+	https://github.com/pysam-developers/pysam
+	https://pypi.python.org/pypi/pysam"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="=sci-libs/htslib-1.5*:="
+DEPEND="${RDEPEND}
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/setuptools[${PYTHON_USEDEP}]"
+
+PATCHES=( "${FILESDIR}"/${PN}-0.12-fix-buildsystem.patch )
+
+python_prepare_all() {
+	# unbundle htslib
+	export HTSLIB_MODE="external"
+	export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include
+	export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir)
+	rm -r htslib || die
+
+	# prevent setup.py from adding RPATHs
+	sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \
+		-i cy_build.py || die
+	sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
+		-i setup.py || die
+
+	distutils-r1_python_prepare_all
+}
+
+src_compile() {
+	# TODO
+	# empty compile, as the build system runs the whole build again in install
+	:
+}