commit: a26495e2ae69026f4ad9d7a730611a1cac92448e Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sat Sep 2 12:33:32 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sat Sep 2 12:35:41 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a26495e2
sci-biology/bcftools: Add 1.5 from sci overlay Package-Manager: Portage-2.3.8, Repoman-2.3.3 sci-biology/bcftools/Manifest | 1 + sci-biology/bcftools/bcftools-1.5.ebuild | 45 ++++++++++++++++++++++ .../bcftools/files/bcftools-1.5-buildsystem.patch | 10 +++++ .../bcftools/files/bcftools-1.5-fix-shebangs.patch | 24 ++++++++++++ sci-biology/bcftools/metadata.xml | 15 ++++++++ 5 files changed, 95 insertions(+) diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest new file mode 100644 index 00000000000..3540e9d20d5 --- /dev/null +++ b/sci-biology/bcftools/Manifest @@ -0,0 +1 @@ +DIST bcftools-1.5.tar.bz2 2975685 SHA256 9ff75a680891467776d7064f41deb6be7a595030ba807494727cd5bee7842301 SHA512 66b8bc61b9fbb381679a6781f77a18f66e8105567992da011413bc573d99b619558a1cf58e9e1373ae347a8b81638dd91977802a07a4578ddc9c61fb53403233 WHIRLPOOL 86b827d91351d8adc026a1d851bb708e35febcc36a947532662857787ec1da6eea2c88a684b15164638b7f9235f6a6f92f4d10618e1719aa891c44c69aaece77 diff --git a/sci-biology/bcftools/bcftools-1.5.ebuild b/sci-biology/bcftools/bcftools-1.5.ebuild new file mode 100644 index 00000000000..9b5df113099 --- /dev/null +++ b/sci-biology/bcftools/bcftools-1.5.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit python-r1 + +DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files" +HOMEPAGE="http://www.htslib.org"; +SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"; + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + dev-lang/perl + =sci-libs/htslib-${PV}*:= + sys-libs/zlib + ${PYTHON_DEPS}" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${PN}-1.5-buildsystem.patch + "${FILESDIR}"/${PN}-1.5-fix-shebangs.patch +) + +src_prepare() { + default + + # remove bundled htslib + rm -r htslib-* || die +} + +src_configure() { + econf \ + --disable-bcftools-plugins \ + --disable-libgsl \ + --disable-configure-htslib \ + --with-htslib=system +} diff --git a/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch b/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch new file mode 100644 index 00000000000..304fc03e744 --- /dev/null +++ b/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch @@ -0,0 +1,10 @@ +--- a/Makefile ++++ b/Makefile +@@ -275,7 +275,6 @@ + $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir) + $(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir) + $(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir) +- $(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir) + + clean: testclean clean-plugins + -rm -f gmon.out *.o *~ $(PROG) version.h plugins/*.so plugins/*.P diff --git a/sci-biology/bcftools/files/bcftools-1.5-fix-shebangs.patch b/sci-biology/bcftools/files/bcftools-1.5-fix-shebangs.patch new file mode 100644 index 00000000000..c6cfc8b991d --- /dev/null +++ b/sci-biology/bcftools/files/bcftools-1.5-fix-shebangs.patch @@ -0,0 +1,24 @@ +--- a/misc/guess-ploidy.py ++++ b/misc/guess-ploidy.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/env python2.7 + # + # Plot the output of "bcftools +guess-ploidy -v" + # +--- a/misc/plot-roh.py ++++ b/misc/plot-roh.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python2.7 + + import glob, gzip, csv, sys, os, copy, re + csv.register_dialect('tab', delimiter='\t', quoting=csv.QUOTE_NONE) +--- a/misc/vcfutils.pl ++++ b/misc/vcfutils.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # Copyright (C) 2010 Broad Institute. + # Copyright (C) 2011, 2014 Genome Research Ltd. diff --git a/sci-biology/bcftools/metadata.xml b/sci-biology/bcftools/metadata.xml new file mode 100644 index 00000000000..4fd13be2f92 --- /dev/null +++ b/sci-biology/bcftools/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biol...@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <maintainer type="person"> + <email>mmokr...@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <upstream> + <remote-id type="github">samtools/bcftools</remote-id> + </upstream> +</pkgmetadata>
