* [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/, sci-biology/pysam/files/
@ 2016-04-09 22:14 David Seifert
0 siblings, 0 replies; 4+ messages in thread
From: David Seifert @ 2016-04-09 22:14 UTC (permalink / raw
To: gentoo-commits
commit: e2ab268997d872b610d931593db890f6c4dc4630
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Apr 9 22:05:20 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Apr 9 22:06:07 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e2ab2689
sci-biology/pysam: Version bump, add py3 support
Package-Manager: portage-2.2.28
sci-biology/pysam/Manifest | 1 +
.../pysam/files/pysam-0.9.0-missing-config.h.patch | 40 +++++++++++++++++++
sci-biology/pysam/pysam-0.9.0.ebuild | 46 ++++++++++++++++++++++
3 files changed, 87 insertions(+)
diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index 4aea08f..b7281db 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1 +1,2 @@
DIST pysam-0.6.tar.gz 841790 SHA256 081c980481f31a81acb06f6fa5638b899321eddfd9eeb5075393e4dad84a1fc8 SHA512 b60df4551600f04e8ae67aec0f2745846d2411e2a1cc4c874ef296ee80ab075256190ebb0ec64eb78231d4d7b59670c5259818cd315f52c923774cc4c0b8b391 WHIRLPOOL eddeb19f3ebf0c6326f7c1b6b7224b2b8cb708e0bf7ceb66b1cac18909abafd1704b264452b70ee6721af4b3b360b51285dcffd7f137c6128920f91dc0dec7b2
+DIST pysam-0.9.0.tar.gz 2701721 SHA256 dd4946c8efa6786a754e2b50c6027dd03aa82c8ee6c2be3b4e51384da80b4c7c SHA512 9189ef2b56df0f5e2c84586c0c2b2cd46a77dbedd3aa6fd25ddcc4a93320038bead073206fff528ae9775f153c875838726dd0af8e4c7bf4e0c6063145e2bc06 WHIRLPOOL 6c7d459057fed3961e983b3e8563e10a47cb87f5da2fb99ca893eff9e19a8b9e4c27b5d82a978a611d615eba8052fbe3e36498ea461e03521a075d9aee8da463
diff --git a/sci-biology/pysam/files/pysam-0.9.0-missing-config.h.patch b/sci-biology/pysam/files/pysam-0.9.0-missing-config.h.patch
new file mode 100644
index 0000000..617786a
--- /dev/null
+++ b/sci-biology/pysam/files/pysam-0.9.0-missing-config.h.patch
@@ -0,0 +1,40 @@
+From 55f5d8ce51ad999123a779f31fcf0fecd60de9e6 Mon Sep 17 00:00:00 2001
+From: Andreas Heger <andreas.heger@gmail.com>
+Date: Mon, 21 Mar 2016 21:10:04 +0000
+Subject: [PATCH] {AH} create empty config.h for samtools if it does not exist,
+ fixes #245
+
+---
+ setup.py | 12 +++++++++++-
+ 1 file changed, 11 insertions(+), 1 deletion(-)
+
+diff --git a/setup.py b/setup.py
+index 7b59b69..2f00c37 100644
+--- a/setup.py
++++ b/setup.py
+@@ -155,7 +155,7 @@ def run_configure(option):
+ outf.write(
+ "/* empty config.h created by pysam */\n")
+ outf.write(
+- "/* conservative compilation options */")
++ "/* conservative compilation options */\n")
+
+ if HTSLIB_LIBRARY_DIR:
+ # linking against a shared, externally installed htslib version, no
+@@ -259,6 +259,16 @@ def run_configure(option):
+ "adding shared libcurl and libcrypto")
+ external_htslib_libraries.extend(["curl", "crypto"])
+
++# create empty config.h files if they have not been created automatically
++# or created by the user:
++for fn in "samtools/config.h", "htslib/config.h":
++ if not os.path.exists(fn):
++ with open(fn, "w") as outf:
++ outf.write(
++ "/* empty config.h created by pysam */\n")
++ outf.write(
++ "/* conservative compilation options */\n")
++
+ parts = ["samtools",
+ "bcftools",
+ "htslib",
diff --git a/sci-biology/pysam/pysam-0.9.0.ebuild b/sci-biology/pysam/pysam-0.9.0.ebuild
new file mode 100644
index 0000000..5fcecfb
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.9.0.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_{4,5} )
+
+inherit distutils-r1 python-r1
+
+DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
+HOMEPAGE="https://github.com/pysam-developers/pysam http://pypi.python.org/pypi/pysam"
+SRC_URI="https://github.com/pysam-developers/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="=sci-libs/htslib-1.3*"
+DEPEND="${RDEPEND}
+ dev-python/cython[${PYTHON_USEDEP}]
+ dev-python/setuptools[${PYTHON_USEDEP}]"
+
+PATCHES=(
+ "${FILESDIR}/${P}-missing-config.h.patch"
+)
+
+src_prepare() {
+ default
+
+ export HTSLIB_INCLUDE_DIR=${EPREFIX}/usr/include
+ export HTSLIB_LIBRARY_DIR=${EPREFIX}/usr/$(get_libdir)
+ export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"
+
+ 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
+}
+
+src_compile() {
+ # TODO
+ # empty compile, as the build system runs the whole build again in install
+ :
+}
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/, sci-biology/pysam/files/
@ 2017-09-02 12:37 David Seifert
0 siblings, 0 replies; 4+ messages in thread
From: David Seifert @ 2017-09-02 12:37 UTC (permalink / raw
To: gentoo-commits
commit: de55574a2c871cd8baaf5fdc33960f90401d3e44
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 2 11:07:41 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep 2 12:36:59 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=de55574a
sci-biology/pysam: Remove old
Package-Manager: Portage-2.3.8, Repoman-2.3.3
Closes: https://github.com/gentoo/gentoo/pull/5593
sci-biology/pysam/Manifest | 1 -
.../pysam/files/pysam-0.9.0-missing-config.h.patch | 40 -------------------
sci-biology/pysam/pysam-0.9.0.ebuild | 45 ----------------------
3 files changed, 86 deletions(-)
diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index b2e7af85717..c95db9a1dcd 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,2 +1 @@
DIST pysam-0.12.tar.gz 2537142 SHA256 33922cb3277ed9a63457c1b6a9dcad2774a217ababcc97a854435be87ba80488 SHA512 095a47cd7258ef093a172445c425f382996da886e44e1beb81ecdec2325024e099d14bee6fcd928c4449099f51ad92b6d7ceb464815c463ab4478f162a40f21e WHIRLPOOL 2331e24d817cd3e7372df8e115498456e685ac426796b29c6d5a28edbaab2321f7efc9db0f14a000750fcd9e30391c02b81e439a07596813bdf7fc6c6e1a3ae3
-DIST pysam-0.9.0.tar.gz 2701721 SHA256 dd4946c8efa6786a754e2b50c6027dd03aa82c8ee6c2be3b4e51384da80b4c7c SHA512 9189ef2b56df0f5e2c84586c0c2b2cd46a77dbedd3aa6fd25ddcc4a93320038bead073206fff528ae9775f153c875838726dd0af8e4c7bf4e0c6063145e2bc06 WHIRLPOOL 6c7d459057fed3961e983b3e8563e10a47cb87f5da2fb99ca893eff9e19a8b9e4c27b5d82a978a611d615eba8052fbe3e36498ea461e03521a075d9aee8da463
diff --git a/sci-biology/pysam/files/pysam-0.9.0-missing-config.h.patch b/sci-biology/pysam/files/pysam-0.9.0-missing-config.h.patch
deleted file mode 100644
index 617786a5a58..00000000000
--- a/sci-biology/pysam/files/pysam-0.9.0-missing-config.h.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-From 55f5d8ce51ad999123a779f31fcf0fecd60de9e6 Mon Sep 17 00:00:00 2001
-From: Andreas Heger <andreas.heger@gmail.com>
-Date: Mon, 21 Mar 2016 21:10:04 +0000
-Subject: [PATCH] {AH} create empty config.h for samtools if it does not exist,
- fixes #245
-
----
- setup.py | 12 +++++++++++-
- 1 file changed, 11 insertions(+), 1 deletion(-)
-
-diff --git a/setup.py b/setup.py
-index 7b59b69..2f00c37 100644
---- a/setup.py
-+++ b/setup.py
-@@ -155,7 +155,7 @@ def run_configure(option):
- outf.write(
- "/* empty config.h created by pysam */\n")
- outf.write(
-- "/* conservative compilation options */")
-+ "/* conservative compilation options */\n")
-
- if HTSLIB_LIBRARY_DIR:
- # linking against a shared, externally installed htslib version, no
-@@ -259,6 +259,16 @@ def run_configure(option):
- "adding shared libcurl and libcrypto")
- external_htslib_libraries.extend(["curl", "crypto"])
-
-+# create empty config.h files if they have not been created automatically
-+# or created by the user:
-+for fn in "samtools/config.h", "htslib/config.h":
-+ if not os.path.exists(fn):
-+ with open(fn, "w") as outf:
-+ outf.write(
-+ "/* empty config.h created by pysam */\n")
-+ outf.write(
-+ "/* conservative compilation options */\n")
-+
- parts = ["samtools",
- "bcftools",
- "htslib",
diff --git a/sci-biology/pysam/pysam-0.9.0.ebuild b/sci-biology/pysam/pysam-0.9.0.ebuild
deleted file mode 100644
index ba886f80899..00000000000
--- a/sci-biology/pysam/pysam-0.9.0.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1 python-r1
-
-DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
-HOMEPAGE="https://github.com/pysam-developers/pysam http://pypi.python.org/pypi/pysam"
-SRC_URI="https://github.com/pysam-developers/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="=sci-libs/htslib-1.3*"
-DEPEND="${RDEPEND}
- dev-python/cython[${PYTHON_USEDEP}]
- dev-python/setuptools[${PYTHON_USEDEP}]"
-
-PATCHES=(
- "${FILESDIR}/${P}-missing-config.h.patch"
-)
-
-src_prepare() {
- default
-
- export HTSLIB_INCLUDE_DIR=${EPREFIX}/usr/include
- export HTSLIB_LIBRARY_DIR=${EPREFIX}/usr/$(get_libdir)
- export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"
-
- 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
-}
-
-src_compile() {
- # TODO
- # empty compile, as the build system runs the whole build again in install
- :
-}
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/, sci-biology/pysam/files/
@ 2017-09-02 18:35 David Seifert
0 siblings, 0 replies; 4+ messages in thread
From: David Seifert @ 2017-09-02 18:35 UTC (permalink / raw
To: gentoo-commits
commit: e4dbb5c139e2c3dfe8a7d6eaa7f19a08da9b88b0
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 2 18:34:46 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep 2 18:35:42 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e4dbb5c1
sci-biology/pysam: Fix broken relative -I
Bug: https://bugs.gentoo.org/show_bug.cgi?id=629670
Package-Manager: Portage-2.3.8, Repoman-2.3.3
.../pysam/files/pysam-0.12-fix-buildsystem.patch | 63 ++++++++++++++++++++++
sci-biology/pysam/pysam-0.12.ebuild | 6 ++-
2 files changed, 68 insertions(+), 1 deletion(-)
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 00000000000..8b323a63fba
--- /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/pysam-0.12.ebuild b/sci-biology/pysam/pysam-0.12.ebuild
index e181e06ac9b..1f4f58fdfe2 100644
--- a/sci-biology/pysam/pysam-0.12.ebuild
+++ b/sci-biology/pysam/pysam-0.12.ebuild
@@ -22,10 +22,14 @@ 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)
- export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"
+ rm -r htslib || die
# prevent setup.py from adding RPATHs
sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/, sci-biology/pysam/files/
@ 2021-10-11 14:55 David Seifert
0 siblings, 0 replies; 4+ messages in thread
From: David Seifert @ 2021-10-11 14:55 UTC (permalink / raw
To: gentoo-commits
commit: 3b93bba18c14598747eda127476f093040e6b3b6
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 11 14:55:08 2021 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Oct 11 14:55:08 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3b93bba1
sci-biology/pysam: drop 0.16.0.1-r1
Closes: https://bugs.gentoo.org/812242
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/pysam/Manifest | 1 -
.../pysam/files/pysam-0.16.0.1-fix-tests.patch | 37 -------------
sci-biology/pysam/pysam-0.16.0.1-r1.ebuild | 60 ----------------------
3 files changed, 98 deletions(-)
diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index 1e305c998da..91ca2cac79c 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,2 +1 @@
-DIST pysam-0.16.0.1.tar.gz 3294073 BLAKE2B 8df1c9b061b0d4b3962ff4b0e30f1589e02d7df41ce362bff861596d3599bf800bb16b2fa4de326fc07102dc7801b48c6b821e5d47e694a3536bec2c5b1cfece SHA512 5cebb9f3bc8dc6186a629e91423a3c8cb802af6529b943fcd880e056661ec6ee2a00de789cf144c9e40b9d1ef2459c0e06ce27a1b9eab8e2875d2087f275af28
DIST pysam-0.17.0.tar.gz 3579324 BLAKE2B 6b88fe771350f20fa7c90a4c02c60fefd6a34d979c687fce1e34a17e1ff203c7d2d07e36b64f7a73f99676b805334df7f049932ce15e26362a5214da03435d64 SHA512 16740f08fb68a1f24656454b834dd9ac52ad9f864f307564566fc244bbd2efb7cb17107b2e85ca5c56af817918a138d1c071533de1b80e5bba42b01bbad7f552
diff --git a/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch b/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch
deleted file mode 100644
index 9d269878e65..00000000000
--- a/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch
+++ /dev/null
@@ -1,37 +0,0 @@
---- a/tests/pysam_data/Makefile
-+++ b/tests/pysam_data/Makefile
-@@ -3,7 +3,7 @@
- BAI=$(BAM:%.bam=%.bam.bai)
- CRAM=ex1.cram ex2.cram ex3.cram
- CRAI=$(CRAM:%.cram=%.cram.crai)
--NO_PG:=$(findstring --no-PG,$(shell samtools view))
-+NO_PG:=--no-PG
-
- # ex2.bam - bam file without index
-
---- a/tests/tabix_test.py
-+++ b/tests/tabix_test.py
-@@ -14,6 +14,7 @@
- import subprocess
- import glob
- import re
-+import pytest
- from TestUtils import checkBinaryEqual, checkGZBinaryEqual, check_url, \
- load_and_convert, TABIX_DATADIR, get_temp_filename
-
-@@ -1014,6 +1015,7 @@
- globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,))
-
-
-+@pytest.mark.skip(reason="requires internet connectivity")
- class TestRemoteFileHTTP(unittest.TestCase):
-
- url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz"
-@@ -1053,6 +1055,7 @@
- self.assertEqual(list(self.local_file.header), [])
-
-
-+@pytest.mark.skip(reason="requires internet connectivity")
- class TestRemoteFileHTTPWithHeader(TestRemoteFileHTTP):
-
- url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example_comments.gtf.gz"
diff --git a/sci-biology/pysam/pysam-0.16.0.1-r1.ebuild b/sci-biology/pysam/pysam-0.16.0.1-r1.ebuild
deleted file mode 100644
index e27c998bb91..00000000000
--- a/sci-biology/pysam/pysam-0.16.0.1-r1.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
-HOMEPAGE="
- https://github.com/pysam-developers/pysam
- https://pypi.org/project/pysam/"
-SRC_URI="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="=sci-libs/htslib-1.10*:="
-DEPEND="${RDEPEND}"
-BDEPEND="
- dev-python/cython[${PYTHON_USEDEP}]
- <dev-python/setuptools-58[${PYTHON_USEDEP}]
- test? (
- =sci-biology/bcftools-1.10*
- =sci-biology/samtools-1.10*
- )"
-
-distutils_enable_tests pytest
-
-DISTUTILS_IN_SOURCE_BUILD=1
-
-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 (except $ORIGIN)
- sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
- -i setup.py || die
-
- eapply "${FILESDIR}"/${PN}-0.16.0.1-fix-tests.patch
-
- if use test; then
- einfo "Building test data"
- emake -C tests/pysam_data
- emake -C tests/cbcf_data
- fi
-
- distutils-r1_python_prepare_all
-}
-
-python_compile() {
- # breaks with parallel build
- local MAKEOPTS=-j1
- distutils-r1_python_compile
-}
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