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