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

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

commit:     0663dbd3daa9a4f9716f1238a3248e23a97767fa
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 26 11:06:21 2024 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Tue Mar 26 11:06:21 2024 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0663dbd3

sci-biology/samtools: add 1.19.2

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

 sci-biology/samtools/Manifest               |  1 +
 sci-biology/samtools/samtools-1.19.2.ebuild | 47 +++++++++++++++++++++++++++++
 2 files changed, 48 insertions(+)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 72408c9c9544..09cffe1bb5b0 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1 +1,2 @@
 DIST samtools-1.17.tar.bz2 8605080 BLAKE2B 09cb0bff7bf7113a77f57fdb879765b28b65461a574e4a1ab20ae2327af46e5616e04f03eb68706d42ba0643e887d7921974a3d78c5f87d296a4c3b691215260 SHA512 107a6df858c6bd2556ba4e86cc1922c3184df095f347039fa94bfd24e5ee21e1a4a9fba5a7cce248a06ad47f99978d9aae570efee7e30e165f33ea848a2cd3c3
+DIST samtools-1.19.2.tar.bz2 9150483 BLAKE2B fb845b2ccd61f1731ef4cdc180f4b9a4ac75e8c73c1ceaa9409b99e8052ca66b88c73fc71fd1067942aa24964f6df8dcb2d93631e5757e0cc200d7a3b9fad461 SHA512 c08d729fed21112855e0acc9cf7f29c7670d38a02ad6b0f2e9b9ef15a18f07e3e194cc4f6913481c98cd3e85dd4dc975dac96155b892da58bbe8ea3679a5270f

diff --git a/sci-biology/samtools/samtools-1.19.2.ebuild b/sci-biology/samtools/samtools-1.19.2.ebuild
new file mode 100644
index 000000000000..42879b0f8698
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.19.2.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2024 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
+}