[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

["David Seifert" <soap@gentoo.org>]

commit:     6664bbc7a20e0e9662de517ff7aced5dbc2fde9c
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 30 11:10:59 2023 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Mar 30 11:10:59 2023 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6664bbc7

sci-biology/samtools: add 1.17

Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/samtools/Manifest             |  1 +
 sci-biology/samtools/samtools-1.17.ebuild | 47 +++++++++++++++++++++++++++++++
 2 files changed, 48 insertions(+)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 098c93fb112b..d6c2ed1c0762 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-1.16.1.tar.bz2 8217689 BLAKE2B 51ca62655d1f43dd0c6f9bd38b323b8a9d8f7486ce42496e21186da06ea881d94e096214720f3fb8d1dd12d7a23881bc3b25e27b1a845d56157ac7ffda7130c1 SHA512 f9d6b8652234c782a1b369f028073ad4a66c44e9620ae60f0ecb35e0874f04ca633713078b692fdc1a1cc4f884ebdbf3ecae6881f11fb3b4fd3d27c5b8da67ba
+DIST samtools-1.17.tar.bz2 8605080 BLAKE2B 09cb0bff7bf7113a77f57fdb879765b28b65461a574e4a1ab20ae2327af46e5616e04f03eb68706d42ba0643e887d7921974a3d78c5f87d296a4c3b691215260 SHA512 107a6df858c6bd2556ba4e86cc1922c3184df095f347039fa94bfd24e5ee21e1a4a9fba5a7cce248a06ad47f99978d9aae570efee7e30e165f33ea848a2cd3c3

diff --git a/sci-biology/samtools/samtools-1.17.ebuild b/sci-biology/samtools/samtools-1.17.ebuild
new file mode 100644
index 000000000000..e105621c7865
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.17.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2023 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="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+
+RDEPEND="
+	dev-lang/perl
+	=sci-libs/htslib-$(ver_cut 1-2)*:=
+	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
+}