commit: e728877de767757bdff23a79092cf0fa15cf5d8a Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Oct 3 17:41:37 2021 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Oct 3 17:41:37 2021 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e728877d
sci-biology/samtools: add 1.13 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/samtools/Manifest | 1 + sci-biology/samtools/samtools-1.13.ebuild | 47 +++++++++++++++++++++++++++++++ 2 files changed, 48 insertions(+) diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest index 622e57502c3..2128bb6db9c 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 00000000000..3165c7b7381 --- /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 +}
