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commit: 4647f40e12c546cd0b18b1966acd944fc8a21641 |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Fri Mar 31 21:00:05 2017 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Fri Mar 31 21:00:05 2017 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4647f40e |
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|
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Revert "sci-biology/deeptools: add a new package" |
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|
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This reverts commit 81a1355ea065924e0c6426772af7c16d90432ccd. |
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|
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dev-python/pyBigWig/metadata.xml | 12 ---- |
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dev-python/pyBigWig/pyBigWig-0.3.4.ebuild | 16 ----- |
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dev-python/pyBigWig/pyBigWig-9999.ebuild | 18 ------ |
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sci-biology/deeptools/deeptools-2.5.0.ebuild | 33 ---------- |
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sci-biology/deeptools/deeptools-9999.ebuild | 34 ---------- |
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sci-biology/deeptools/metadata.xml | 12 ---- |
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sci-biology/mira/mira-4.9.6.ebuild | 93 ---------------------------- |
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sci-biology/plinkseq/plinkseq-9999.ebuild | 13 ++-- |
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8 files changed, 5 insertions(+), 226 deletions(-) |
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|
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diff --git a/dev-python/pyBigWig/metadata.xml b/dev-python/pyBigWig/metadata.xml |
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deleted file mode 100644 |
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index f68a1b6fa..000000000 |
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--- a/dev-python/pyBigWig/metadata.xml |
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+++ /dev/null |
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@@ -1,12 +0,0 @@ |
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-<?xml version="1.0" encoding="UTF-8"?> |
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-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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-<pkgmetadata> |
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- <maintainer type="person"> |
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- <email>mmokrejs@×××××××××××××××.cz</email> |
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- <name>Martin Mokrejs</name> |
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- </maintainer> |
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- <maintainer type="project"> |
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- <email>sci-biology@g.o</email> |
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- <name>Gentoo Biology Project</name> |
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- </maintainer> |
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-</pkgmetadata> |
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|
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diff --git a/dev-python/pyBigWig/pyBigWig-0.3.4.ebuild b/dev-python/pyBigWig/pyBigWig-0.3.4.ebuild |
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deleted file mode 100644 |
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index 33664c388..000000000 |
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--- a/dev-python/pyBigWig/pyBigWig-0.3.4.ebuild |
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+++ /dev/null |
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@@ -1,16 +0,0 @@ |
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-# Copyright 1999-2017 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=5 |
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- |
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-DESCRIPTION="Python extension written in C for quick access to and creation of bigWig files" |
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-HOMEPAGE="https://github.com/dpryan79/pyBigWig" |
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-SRC_URI="https://github.com/dpryan79/pyBigWig/archive/0.3.4.tar.gz -> ${P}.tar.gz" |
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- |
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-LICENSE="MIT" |
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-SLOT="0" |
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-KEYWORDS="~amd64 ~x86" |
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-IUSE="" |
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- |
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-DEPEND="sci-biology/libBigWig" |
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-RDEPEND="${DEPEND}" |
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|
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diff --git a/dev-python/pyBigWig/pyBigWig-9999.ebuild b/dev-python/pyBigWig/pyBigWig-9999.ebuild |
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deleted file mode 100644 |
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index 0e2cd40c8..000000000 |
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--- a/dev-python/pyBigWig/pyBigWig-9999.ebuild |
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+++ /dev/null |
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@@ -1,18 +0,0 @@ |
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-# Copyright 1999-2017 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=5 |
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- |
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-inherit git-r3 |
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- |
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-DESCRIPTION="Python extension written in C for quick access to and creation of bigWig files" |
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-HOMEPAGE="https://github.com/dpryan79/pyBigWig" |
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-EGIT_REPO_URI="https://github.com/dpryan79/pyBigWig.git" |
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- |
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-LICENSE="MIT" |
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-SLOT="0" |
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-KEYWORDS="" |
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-IUSE="" |
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- |
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-DEPEND="sci-biology/libBigWig" |
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-RDEPEND="${DEPEND}" |
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|
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diff --git a/sci-biology/deeptools/deeptools-2.5.0.ebuild b/sci-biology/deeptools/deeptools-2.5.0.ebuild |
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deleted file mode 100644 |
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index 6f9a41d54..000000000 |
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--- a/sci-biology/deeptools/deeptools-2.5.0.ebuild |
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+++ /dev/null |
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@@ -1,33 +0,0 @@ |
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-# Copyright 1999-2017 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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- |
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-EAPI=5 |
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- |
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-PYTHON_COMPAT=( python2_7 python3_5 ) |
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- |
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-inherit distutils-r1 |
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- |
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-[ "$PV" == "9999" ] && inherit git-2 |
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- |
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-DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig" |
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-HOMEPAGE="https://github.com/fidelram/deepTools" |
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-if [ "$PV" == "9999" ]; then |
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- EGIT_REPO_URI="https://github.com/fidelram/deepTools" |
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- KEYWORDS="" |
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-else |
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- SRC_URI="https://github.com/fidelram/deepTools/archive/2.5.0.tar.gz -> ${P}.tar.gz" |
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- KEYWORDS="~amd64" |
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-fi |
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- |
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-LICENSE="GPL-3" |
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-SLOT="0" |
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-IUSE="" |
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- |
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-DEPEND=">=dev-python/numpy-1.8.0 |
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- >=sci-libs/scipy-0.17.0 |
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- >=dev-python/py2bit-0.1.0 |
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- >=dev-python/pyBigWig-0.2.1 |
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- >=sci-biology/pysam-0.8 |
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- >=dev-python/matplotlib-1.4.0" |
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-RDEPEND="${DEPEND}" |
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- |
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|
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diff --git a/sci-biology/deeptools/deeptools-9999.ebuild b/sci-biology/deeptools/deeptools-9999.ebuild |
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deleted file mode 100644 |
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index 4d6d2fa77..000000000 |
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--- a/sci-biology/deeptools/deeptools-9999.ebuild |
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+++ /dev/null |
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@@ -1,34 +0,0 @@ |
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-# Copyright 1999-2017 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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-# $Id$ |
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- |
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-EAPI=5 |
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- |
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-PYTHON_COMPAT=( python2_7 python3_5 ) |
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- |
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-inherit distutils-r1 |
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- |
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-[ "$PV" == "9999" ] && inherit git-2 |
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- |
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-DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig" |
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-HOMEPAGE="https://github.com/fidelram/deepTools" |
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-if [ "$PV" == "9999" ]; then |
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- EGIT_REPO_URI="https://github.com/fidelram/deepTools" |
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- KEYWORDS="" |
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-else |
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- SRC_URI="https://github.com/fidelram/deepTools/archive/2.5.0.tar.gz -> ${P}.tar.gz" |
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- KEYWORDS="~amd64" |
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-fi |
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- |
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-LICENSE="GPL-3" |
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-SLOT="0" |
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-IUSE="" |
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- |
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-DEPEND=">=dev-python/numpy-1.8.0 |
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- >=sci-libs/scipy-0.17.0 |
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- >=dev-python/py2bit-0.1.0 |
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- >=dev-python/pyBigWig-0.2.1 |
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- >=sci-biology/pysam-0.8 |
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- >=dev-python/matplotlib-1.4.0" |
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-RDEPEND="${DEPEND}" |
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- |
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|
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diff --git a/sci-biology/deeptools/metadata.xml b/sci-biology/deeptools/metadata.xml |
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deleted file mode 100644 |
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index f68a1b6fa..000000000 |
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--- a/sci-biology/deeptools/metadata.xml |
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+++ /dev/null |
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@@ -1,12 +0,0 @@ |
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-<?xml version="1.0" encoding="UTF-8"?> |
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-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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-<pkgmetadata> |
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- <maintainer type="person"> |
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- <email>mmokrejs@×××××××××××××××.cz</email> |
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- <name>Martin Mokrejs</name> |
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- </maintainer> |
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- <maintainer type="project"> |
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- <email>sci-biology@g.o</email> |
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- <name>Gentoo Biology Project</name> |
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- </maintainer> |
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-</pkgmetadata> |
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|
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diff --git a/sci-biology/mira/mira-4.9.6.ebuild b/sci-biology/mira/mira-4.9.6.ebuild |
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deleted file mode 100644 |
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index 22ddea015..000000000 |
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--- a/sci-biology/mira/mira-4.9.6.ebuild |
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+++ /dev/null |
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@@ -1,93 +0,0 @@ |
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-# Copyright 1999-2015 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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-# $Id$ |
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- |
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-EAPI=5 |
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- |
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-MIRA_3RDPARTY_PV="06-07-2012" |
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-MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat) |
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- |
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-inherit autotools eutils multilib |
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- |
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-DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina" |
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-HOMEPAGE="http://www.chevreux.org/projects_mira.html" |
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-SRC_URI=" |
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- http://sourceforge.net/projects/mira-assembler/files/MIRA/development/"${PN}"-"${MY_PV}".tar.bz2 |
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- mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" |
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-# http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2 |
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-# http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2 |
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-# mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" |
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- |
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-S="${WORKDIR}"/"${PN}"-"${MY_PV}" |
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- |
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-SLOT="0" |
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-LICENSE="GPL-2" |
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-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" |
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-IUSE="doc" |
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- |
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-CDEPEND=" |
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- dev-libs/boost |
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- dev-util/google-perftools" |
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-DEPEND="${CDEPEND} |
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- app-editors/vim-core |
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- dev-libs/expat" |
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-RDEPEND="${CDEPEND}" |
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- |
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-#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED |
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-# THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf ) |
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-DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS ) |
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- |
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-# mira 4.9.x requires C++14 standard compliant compiler, so >=gcc-4.9.1 |
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-src_prepare() { |
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- find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die |
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- epatch \ |
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- "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch \ |
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- "${FILESDIR}"/${P}-cout.patch \ |
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- "${FILESDIR}"/${P}-DESTDIR.patch |
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- |
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- sed \ |
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- -e "s:-O[23]::g" \ |
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- -e "s:-funroll-loops::g" \ |
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- -i configure.ac || die |
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- |
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- eautoreconf |
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-} |
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- |
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-src_configure() { |
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- econf \ |
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- --with-boost="${EPREFIX}/usr/$(get_libdir)" \ |
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- --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \ |
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- --with-boost-thread=boost_thread-mt |
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-} |
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- |
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-#src_compile() { |
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-# base_src_compile |
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-# # TODO: resolve docbook incompatibility for building docs |
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-# if use doc; then emake -C doc clean docs || die; fi |
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-#} |
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- |
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-src_install() { |
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- default |
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- dodoc ${DOCS[@]} |
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- |
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- dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} |
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- dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta} |
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- |
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- # if sci-biology/staden is installed, ideally use configprotect? |
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- if [ -e "${ED}"/usr/share/staden/etc/GTAGDB ]; then |
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- if [ `grep -c HAF "${ED}"/usr/share/staden/etc/GTAGDB` -eq 0 ]; then |
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- cat "${ED}"/usr/share/staden/etc/GTAGDB "${S}"/src/support/GTAGDB > "${WORKDIR}"/GTAGDB || die |
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- insinto /usr/share/staden/etc/ |
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- doins "${WORKDIR}"/GTAGDB |
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- fi |
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- fi |
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- if [ -e "/etc/consedrc/" ]; then |
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- insinto /etc/consedrc |
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- doins "${S}"/src/support/consedtaglib.txt |
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- fi |
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-} |
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- |
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-pkg_postinst() { |
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- einfo "Documentation is no longer built, you can find it at:" |
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- einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html" |
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-} |
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|
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diff --git a/sci-biology/plinkseq/plinkseq-9999.ebuild b/sci-biology/plinkseq/plinkseq-9999.ebuild |
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index cffdaff97..461e62f84 100644 |
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--- a/sci-biology/plinkseq/plinkseq-9999.ebuild |
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+++ b/sci-biology/plinkseq/plinkseq-9999.ebuild |
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@@ -20,6 +20,7 @@ IUSE="" |
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|
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DEPEND="sys-libs/zlib |
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dev-libs/protobuf |
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+ www-servers/mongoose |
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!sci-biology/fsl" # file collision on /usr/bin/mm |
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RDEPEND="${DEPEND}" |
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|
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@@ -28,9 +29,7 @@ src_prepare(){ |
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sed -e "s/= -static/=/g" -i config_defs.Makefile || die |
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rm -rf sources/ext/protobuf-* || die |
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rm sources/ext/protobuf sources/ext/sources/include/google || die |
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- # we cannot zap calls to bundled mongoose because www-servers/mongoose does not build a library at all |
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- # rm -rf sources/mongoose || die |
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- # sed -e "s@$(MONGOOSE_LIB_DIR) @@;s@$(MONGOOSE_INC) @@;s@$(MONGOOSE_LIB_BASE_DIR) @@" - Makefile || die |
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+ rm -rf sources/mongoose || die |
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sed -e 's@^all:.*@all: # skipping compilation of bundled dev-libs/protobuf@' -i sources/ext/Makefile || die |
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find . -name \*.proto | while read f; do \ |
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d=`dirname $f`; \ |
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@@ -45,13 +44,11 @@ src_prepare(){ |
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sed -e 's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g' -i sources/plinkseq/sources/lib/matrix.pb.cpp || die |
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sed -e 's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g' -i sources/plinkseq/sources/lib/variant.pb.cpp || die |
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local myinc=`pkg-config protobuf --variable=includedir` |
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- sed -e 's@$(PROTOBUF_LIB_BASE_DIR)/$(INC_DIR)/@'"${myinc}@" -i Makefile || die |
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+ sed -e "s@\$(PROTOBUF_LIB_BASE_DIR)/\$(INC_DIR)/@$myinc@" -i Makefile || die |
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local mylib=`pkg-config protobuf --variable=libdir` |
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- sed -e 's@$(PROTOBUF_LIB_BASE_DIR)/$(BLD_LIB_DIR)/@'"-L${mylib} @" -i Makefile || die # note the trailing space as it get prepended to PROTOBUF_LIBS |
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- # anyway $(PROTOBUF_LIB_FULL_PATH) is a necessary build target, just drop it |
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- sed -e 's@^PROTOBUF_LIB_FULL_PATH =.*/@PROTOBUF_LIB_FULL_PATH =@' -i Makefile || die |
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+ sed -e "s@$(PROTOBUF_LIB_BASE_DIR)/$(BLD_LIB_DIR)/@$mylib@" -i Makefile || die |
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local mylibs=`pkg-config protobuf --libs` |
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- sed -e "s@libprotobuf.a@ ${mylibs}@ " -i Makefile || die |
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+ sed -e "s@libprotobuf.a@$mylibs@" -i Makefile || die |
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} |
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|
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src_install(){ |