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commit: de55574a2c871cd8baaf5fdc33960f90401d3e44 |
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Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Sat Sep 2 11:07:41 2017 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Sat Sep 2 12:36:59 2017 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=de55574a |
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|
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sci-biology/pysam: Remove old |
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|
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Package-Manager: Portage-2.3.8, Repoman-2.3.3 |
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Closes: https://github.com/gentoo/gentoo/pull/5593 |
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|
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sci-biology/pysam/Manifest | 1 - |
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.../pysam/files/pysam-0.9.0-missing-config.h.patch | 40 ------------------- |
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sci-biology/pysam/pysam-0.9.0.ebuild | 45 ---------------------- |
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3 files changed, 86 deletions(-) |
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|
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diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest |
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index b2e7af85717..c95db9a1dcd 100644 |
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--- a/sci-biology/pysam/Manifest |
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+++ b/sci-biology/pysam/Manifest |
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@@ -1,2 +1 @@ |
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DIST pysam-0.12.tar.gz 2537142 SHA256 33922cb3277ed9a63457c1b6a9dcad2774a217ababcc97a854435be87ba80488 SHA512 095a47cd7258ef093a172445c425f382996da886e44e1beb81ecdec2325024e099d14bee6fcd928c4449099f51ad92b6d7ceb464815c463ab4478f162a40f21e WHIRLPOOL 2331e24d817cd3e7372df8e115498456e685ac426796b29c6d5a28edbaab2321f7efc9db0f14a000750fcd9e30391c02b81e439a07596813bdf7fc6c6e1a3ae3 |
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-DIST pysam-0.9.0.tar.gz 2701721 SHA256 dd4946c8efa6786a754e2b50c6027dd03aa82c8ee6c2be3b4e51384da80b4c7c SHA512 9189ef2b56df0f5e2c84586c0c2b2cd46a77dbedd3aa6fd25ddcc4a93320038bead073206fff528ae9775f153c875838726dd0af8e4c7bf4e0c6063145e2bc06 WHIRLPOOL 6c7d459057fed3961e983b3e8563e10a47cb87f5da2fb99ca893eff9e19a8b9e4c27b5d82a978a611d615eba8052fbe3e36498ea461e03521a075d9aee8da463 |
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|
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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 |
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deleted file mode 100644 |
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index 617786a5a58..00000000000 |
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--- a/sci-biology/pysam/files/pysam-0.9.0-missing-config.h.patch |
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+++ /dev/null |
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@@ -1,40 +0,0 @@ |
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-From 55f5d8ce51ad999123a779f31fcf0fecd60de9e6 Mon Sep 17 00:00:00 2001 |
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-From: Andreas Heger <andreas.heger@×××××.com> |
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-Date: Mon, 21 Mar 2016 21:10:04 +0000 |
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-Subject: [PATCH] {AH} create empty config.h for samtools if it does not exist, |
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- fixes #245 |
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- |
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---- |
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- setup.py | 12 +++++++++++- |
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- 1 file changed, 11 insertions(+), 1 deletion(-) |
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- |
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-diff --git a/setup.py b/setup.py |
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-index 7b59b69..2f00c37 100644 |
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---- a/setup.py |
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-+++ b/setup.py |
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-@@ -155,7 +155,7 @@ def run_configure(option): |
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- outf.write( |
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- "/* empty config.h created by pysam */\n") |
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- outf.write( |
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-- "/* conservative compilation options */") |
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-+ "/* conservative compilation options */\n") |
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- |
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- if HTSLIB_LIBRARY_DIR: |
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- # linking against a shared, externally installed htslib version, no |
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-@@ -259,6 +259,16 @@ def run_configure(option): |
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- "adding shared libcurl and libcrypto") |
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- external_htslib_libraries.extend(["curl", "crypto"]) |
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- |
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-+# create empty config.h files if they have not been created automatically |
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-+# or created by the user: |
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-+for fn in "samtools/config.h", "htslib/config.h": |
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-+ if not os.path.exists(fn): |
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-+ with open(fn, "w") as outf: |
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-+ outf.write( |
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-+ "/* empty config.h created by pysam */\n") |
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-+ outf.write( |
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-+ "/* conservative compilation options */\n") |
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-+ |
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- parts = ["samtools", |
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- "bcftools", |
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- "htslib", |
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|
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diff --git a/sci-biology/pysam/pysam-0.9.0.ebuild b/sci-biology/pysam/pysam-0.9.0.ebuild |
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deleted file mode 100644 |
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index ba886f80899..00000000000 |
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--- a/sci-biology/pysam/pysam-0.9.0.ebuild |
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+++ /dev/null |
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@@ -1,45 +0,0 @@ |
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-# Copyright 1999-2016 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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- |
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-EAPI=6 |
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- |
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-PYTHON_COMPAT=( python2_7 python3_{4,5} ) |
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- |
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-inherit distutils-r1 python-r1 |
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- |
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-DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format" |
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-HOMEPAGE="https://github.com/pysam-developers/pysam http://pypi.python.org/pypi/pysam" |
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-SRC_URI="https://github.com/pysam-developers/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" |
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- |
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-LICENSE="MIT" |
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-SLOT="0" |
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-KEYWORDS="~amd64 ~x86" |
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-IUSE="" |
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- |
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-RDEPEND="=sci-libs/htslib-1.3*" |
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-DEPEND="${RDEPEND} |
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- dev-python/cython[${PYTHON_USEDEP}] |
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- dev-python/setuptools[${PYTHON_USEDEP}]" |
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- |
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-PATCHES=( |
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- "${FILESDIR}/${P}-missing-config.h.patch" |
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-) |
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- |
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-src_prepare() { |
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- default |
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- |
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- export HTSLIB_INCLUDE_DIR=${EPREFIX}/usr/include |
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- export HTSLIB_LIBRARY_DIR=${EPREFIX}/usr/$(get_libdir) |
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- export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl" |
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- |
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- sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \ |
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- -i cy_build.py || die |
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- sed -e '/runtime_library_dirs=htslib_library_dirs/d' \ |
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- -i setup.py || die |
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-} |
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- |
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-src_compile() { |
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- # TODO |
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- # empty compile, as the build system runs the whole build again in install |
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- : |
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-} |