sci-biology/bcftools: Add 1.5 from sci overlay

Package-Manager: Portage-2.3.8, Repoman-2.3.3

5 files changed, 95 insertions, 0 deletions

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
new file mode 100644
index 000000000000..3540e9d20d54
--- /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 000000000000..9b5df1130999
--- /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 000000000000..304fc03e7441
--- /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 000000000000..c6cfc8b991d3
--- /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 000000000000..4fd13be2f922
--- /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-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">samtools/bcftools</remote-id>
+	</upstream>
+</pkgmetadata>