commit: 90c55f4b6812ba59ca61467380f0a153f3ff2edf Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Mon Aug 3 16:54:23 2020 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Mon Aug 3 16:54:23 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=90c55f4b
sci-biology/samtools: Bump to version 1.10 Bug: https://bugs.gentoo.org/728018 Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/samtools/Manifest | 1 + sci-biology/samtools/samtools-1.10.ebuild | 56 +++++++++++++++++++++++++++++++ 2 files changed, 57 insertions(+) diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest index 7ce21379a95..b06f63a40e7 100644 --- a/sci-biology/samtools/Manifest +++ b/sci-biology/samtools/Manifest @@ -1,3 +1,4 @@ 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-1.5.tar.bz2 4190142 BLAKE2B 1d3478f9adf76925a3721e145795ce4a4caf580244f5ba5bc1ddd14d1b13c723c6fddc24cdadf0a23ca5dcd7007a9985f54e7532cb15d5d9433b1164f5a22023 SHA512 ff3e39ba867ecbd88f3363b038508c1557e349ea4223483f8f4ecb17ff8864fb53cd193bc2059a147e30f07395bbf53c8518d0f70219e454375c8bffe56e3059 DIST samtools-1.9.tar.bz2 4440405 BLAKE2B 409265fed9ff3fcd09096c968224499750da69324eeded754e367430c0f53f9246ccc9a31e166f13ea7bc767fefab499bcfda4d008d5ac82971984c67b533aff SHA512 6c8207754615ae8dad84b278f93e7d57eb40b818efb80f6aff6aba22fde5772247724e86596e765791e3175ffbb683393dd3ddfe7681c73eef4eb4f2342bf68f diff --git a/sci-biology/samtools/samtools-1.10.ebuild b/sci-biology/samtools/samtools-1.10.ebuild new file mode 100644 index 00000000000..0ef5e6c19e8 --- /dev/null +++ b/sci-biology/samtools/samtools-1.10.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit autotools 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-${PV}* + sys-libs/ncurses:0=[unicode] + sys-libs/zlib:=" +DEPEND="${RDEPEND}" +BDEPEND="virtual/pkgconfig" + +src_prepare() { + default + + # remove bundled htslib + rm -r htslib-* || die + + eautoreconf +} + +src_configure() { + econf \ + --with-ncurses \ + --with-htslib=system \ + CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw)" +} + +src_compile() { + emake AR="$(tc-getAR)" +} + +src_test() { + # the tview test diffs expect 80-columns output + unset COLUMNS + + default +} + +src_install() { + default + + dodoc -r examples + docompress -x /usr/share/doc/${PF}/examples +}
