From e728877de767757bdff23a79092cf0fa15cf5d8a Mon Sep 17 00:00:00 2001
From: David Seifert <soap@gentoo.org>
Date: Sun, 3 Oct 2021 19:41:37 +0200
Subject: sci-biology/samtools: add 1.13

Signed-off-by: David Seifert <soap@gentoo.org>
---
 sci-biology/samtools/Manifest             |  1 +
 sci-biology/samtools/samtools-1.13.ebuild | 47 +++++++++++++++++++++++++++++++
 2 files changed, 48 insertions(+)
 create mode 100644 sci-biology/samtools/samtools-1.13.ebuild

(limited to 'sci-biology')

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 622e57502c38..2128bb6db9c2 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,2 +1,3 @@
 DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
 DIST samtools-1.10.tar.bz2 4721173 BLAKE2B 103c71ec5740eac151a4fc40d67286ee00123c7befd5f654cf5c89812bda44f82b38ab662a4a3216ac84434cabab49500b903612137f97f89a7ea38063e8fc08 SHA512 828ec2638592b440e06b81eafc57634416ab54dac6caaecb06f22a90e9bf99da1fd8bb54509cb98591899c4e097ac9038ee5d57ea7bfe1a18967cde4018d840a
+DIST samtools-1.13.tar.bz2 7984998 BLAKE2B e46161c43d4ea51c3ef1d9ed74c40c21b70aef80aa903a49b94b3d468f9211e9147281204eb61b9843c071f09ead08c924e3d624d4df76a1d02ba9ceb318399a SHA512 647fbad2935dfc3e4f85da257a6ee59af40078024a3b77f117dada5f55846e381a096db3cf62a63c04ae95dfc9fadb1d515b8d618e6388bc93f0b2ac85eaf6ea
diff --git a/sci-biology/samtools/samtools-1.13.ebuild b/sci-biology/samtools/samtools-1.13.ebuild
new file mode 100644
index 000000000000..3165c7b7381c
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.13.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+
+RDEPEND="
+	dev-lang/perl
+	=sci-libs/htslib-${PV}*:=
+	sys-libs/ncurses:=[unicode(+)]
+	sys-libs/zlib"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+	default
+
+	# remove bundled htslib
+	rm -r htslib-* || die
+}
+
+src_configure() {
+	econf \
+		--with-ncurses \
+		--with-htslib=system \
+		CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
+}
+
+src_compile() {
+	emake AR="$(tc-getAR)"
+}
+
+src_install() {
+	default
+
+	dodoc -r examples
+	docompress -x /usr/share/doc/${PF}/examples
+}
-- 
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