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authorDavid Seifert <soap@gentoo.org>2017-09-02 13:07:41 +0200
committerDavid Seifert <soap@gentoo.org>2017-09-02 14:36:59 +0200
commitde55574a2c871cd8baaf5fdc33960f90401d3e44 (patch)
tree5b98c5d3417feb0f0c8cf52d62d090e432fa69a6
parentsci-biology/bwa: Remove old (diff)
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sci-biology/pysam: Remove old
Package-Manager: Portage-2.3.8, Repoman-2.3.3 Closes: https://github.com/gentoo/gentoo/pull/5593
-rw-r--r--sci-biology/pysam/Manifest1
-rw-r--r--sci-biology/pysam/files/pysam-0.9.0-missing-config.h.patch40
-rw-r--r--sci-biology/pysam/pysam-0.9.0.ebuild45
3 files changed, 0 insertions, 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
- :
-}