From cec8859662ffa14fd17eeb93abd6e9aeb0a088a6 Mon Sep 17 00:00:00 2001
From: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Sun, 24 Jun 2018 10:28:22 +0200
Subject: sci-biology/bwa: version bump

Also fix HOMEPAGE which does not listen on https (anymore?)

Package-Manager: Portage-2.3.40, Repoman-2.3.9
---
 sci-biology/bwa/Manifest                        |  1 +
 sci-biology/bwa/bwa-0.7.17.ebuild               | 34 +++++++++++++++++++++++++
 sci-biology/bwa/files/bwa-0.7.15-Makefile.patch | 27 ++++++++++++++++++++
 sci-biology/bwa/metadata.xml                    | 11 ++++++++
 4 files changed, 73 insertions(+)
 create mode 100644 sci-biology/bwa/Manifest
 create mode 100644 sci-biology/bwa/bwa-0.7.17.ebuild
 create mode 100644 sci-biology/bwa/files/bwa-0.7.15-Makefile.patch
 create mode 100644 sci-biology/bwa/metadata.xml

(limited to 'sci-biology')

diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest
new file mode 100644
index 000000000..d5ec96afa
--- /dev/null
+++ b/sci-biology/bwa/Manifest
@@ -0,0 +1 @@
+DIST bwa-0.7.17.tar.bz2 190908 BLAKE2B d646352719a692d35d39ffcfbdbfdbda5d431f3b89b0d8dbc6abc21b64b249512322b123c95190ad35b65fbf3185ba86e8530d060c222d4b3a1787d338779419 SHA512 67cccfef1c7aa1b5aad6b59a49390e8d96f64320c414bfffacf232aeb08c15861e98be826c1b42b6222d6ff086eeb055b1318ea2e9eebfd87b2365d06fc89802
diff --git a/sci-biology/bwa/bwa-0.7.17.ebuild b/sci-biology/bwa/bwa-0.7.17.ebuild
new file mode 100644
index 000000000..429ba43e6
--- /dev/null
+++ b/sci-biology/bwa/bwa-0.7.17.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner"
+HOMEPAGE="http://bio-bwa.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86 ~x64-macos"
+
+RDEPEND="dev-lang/perl"
+
+PATCHES=( "${FILESDIR}"/${PN}-0.7.15-Makefile.patch )
+DOCS=( NEWS.md README-alt.md README.md )
+
+src_configure() {
+	tc-export CC AR
+}
+
+src_install() {
+	dobin bwa
+
+	exeinto /usr/libexec/${PN}
+	doexe qualfa2fq.pl xa2multi.pl
+
+	einstalldocs
+	doman bwa.1
+}
diff --git a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch
new file mode 100644
index 000000000..39b437a02
--- /dev/null
+++ b/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch
@@ -0,0 +1,27 @@
+--- bwa-0.7.13/Makefile
++++ bwa-0.7.13/Makefile
+@@ -1,8 +1,8 @@
+-CC=			gcc
++CC?=			gcc
+ #CC=			clang --analyze
+-CFLAGS=		-g -Wall -Wno-unused-function -O2
++CFLAGS?=		-g -Wall -Wno-unused-function -O2
+ WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
+-AR=			ar
++AR?=			ar
+ DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
+ LOBJS=		utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
+ AOBJS=		QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
+@@ -26,10 +26,10 @@
+ all:$(PROG)
+ 
+ bwa:libbwa.a $(AOBJS) main.o
+-		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
++		$(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
+ 
+ bwamem-lite:libbwa.a example.o
+-		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
++		$(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
+ 
+ libbwa.a:$(LOBJS)
+ 		$(AR) -csru $@ $(LOBJS)
diff --git a/sci-biology/bwa/metadata.xml b/sci-biology/bwa/metadata.xml
new file mode 100644
index 000000000..ceb43ead2
--- /dev/null
+++ b/sci-biology/bwa/metadata.xml
@@ -0,0 +1,11 @@
+<?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>
+  <upstream>
+    <remote-id type="sourceforge">bio-bwa</remote-id>
+  </upstream>
+</pkgmetadata>
-- 
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