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commit: 90c55f4b6812ba59ca61467380f0a153f3ff2edf |
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Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Mon Aug 3 16:54:23 2020 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Mon Aug 3 16:54:23 2020 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=90c55f4b |
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|
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sci-biology/samtools: Bump to version 1.10 |
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|
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Bug: https://bugs.gentoo.org/728018 |
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Package-Manager: Portage-3.0.1, Repoman-2.3.23 |
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Signed-off-by: David Seifert <soap <AT> gentoo.org> |
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|
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sci-biology/samtools/Manifest | 1 + |
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sci-biology/samtools/samtools-1.10.ebuild | 56 +++++++++++++++++++++++++++++++ |
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2 files changed, 57 insertions(+) |
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|
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diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest |
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index 7ce21379a95..b06f63a40e7 100644 |
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--- a/sci-biology/samtools/Manifest |
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+++ b/sci-biology/samtools/Manifest |
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@@ -1,3 +1,4 @@ |
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DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5 |
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+DIST samtools-1.10.tar.bz2 4721173 BLAKE2B 103c71ec5740eac151a4fc40d67286ee00123c7befd5f654cf5c89812bda44f82b38ab662a4a3216ac84434cabab49500b903612137f97f89a7ea38063e8fc08 SHA512 828ec2638592b440e06b81eafc57634416ab54dac6caaecb06f22a90e9bf99da1fd8bb54509cb98591899c4e097ac9038ee5d57ea7bfe1a18967cde4018d840a |
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DIST samtools-1.5.tar.bz2 4190142 BLAKE2B 1d3478f9adf76925a3721e145795ce4a4caf580244f5ba5bc1ddd14d1b13c723c6fddc24cdadf0a23ca5dcd7007a9985f54e7532cb15d5d9433b1164f5a22023 SHA512 ff3e39ba867ecbd88f3363b038508c1557e349ea4223483f8f4ecb17ff8864fb53cd193bc2059a147e30f07395bbf53c8518d0f70219e454375c8bffe56e3059 |
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DIST samtools-1.9.tar.bz2 4440405 BLAKE2B 409265fed9ff3fcd09096c968224499750da69324eeded754e367430c0f53f9246ccc9a31e166f13ea7bc767fefab499bcfda4d008d5ac82971984c67b533aff SHA512 6c8207754615ae8dad84b278f93e7d57eb40b818efb80f6aff6aba22fde5772247724e86596e765791e3175ffbb683393dd3ddfe7681c73eef4eb4f2342bf68f |
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|
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diff --git a/sci-biology/samtools/samtools-1.10.ebuild b/sci-biology/samtools/samtools-1.10.ebuild |
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new file mode 100644 |
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index 00000000000..0ef5e6c19e8 |
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--- /dev/null |
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+++ b/sci-biology/samtools/samtools-1.10.ebuild |
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@@ -0,0 +1,56 @@ |
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+# Copyright 1999-2020 Gentoo Authors |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
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+EAPI=7 |
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+ |
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+inherit autotools toolchain-funcs |
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+ |
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+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" |
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+HOMEPAGE="http://www.htslib.org/" |
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+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" |
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+ |
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+LICENSE="MIT" |
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+SLOT="0" |
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+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
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+ |
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+RDEPEND=" |
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+ dev-lang/perl |
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+ =sci-libs/htslib-${PV}* |
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+ sys-libs/ncurses:0=[unicode] |
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+ sys-libs/zlib:=" |
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+DEPEND="${RDEPEND}" |
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+BDEPEND="virtual/pkgconfig" |
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+ |
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+src_prepare() { |
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+ default |
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+ |
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+ # remove bundled htslib |
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+ rm -r htslib-* || die |
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+ |
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+ eautoreconf |
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+} |
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+ |
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+src_configure() { |
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+ econf \ |
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+ --with-ncurses \ |
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+ --with-htslib=system \ |
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+ CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw)" |
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+} |
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+ |
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+src_compile() { |
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+ emake AR="$(tc-getAR)" |
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+} |
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+ |
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+src_test() { |
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+ # the tview test diffs expect 80-columns output |
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+ unset COLUMNS |
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+ |
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+ default |
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+} |
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+ |
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+src_install() { |
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+ default |
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+ |
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+ dodoc -r examples |
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+ docompress -x /usr/share/doc/${PF}/examples |
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+} |