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commit: 369678cffc9f7ecae414f3800f01a2c2251e8669 |
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Author: Justin Lecher <jlec <AT> gentoo <DOT> org> |
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AuthorDate: Sat Dec 26 18:02:47 2015 +0000 |
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Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> |
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CommitDate: Sat Dec 26 18:02:47 2015 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=369678cf |
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|
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sci-biology/bowtie: Drop old |
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|
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obsoletes: |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=564320 |
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|
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Package-Manager: portage-2.2.26 |
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Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> |
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|
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sci-biology/bowtie/Manifest | 1 - |
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sci-biology/bowtie/bowtie-0.12.8.ebuild | 44 --------------------- |
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.../bowtie/files/bowtie-0.12.8-gcc-47.patch | 45 ---------------------- |
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3 files changed, 90 deletions(-) |
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|
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diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest |
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index c692c89..1291400 100644 |
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--- a/sci-biology/bowtie/Manifest |
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+++ b/sci-biology/bowtie/Manifest |
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@@ -1,3 +1,2 @@ |
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-DIST bowtie-0.12.8-src.zip 15569919 SHA256 f074a0f25e156976c4951fd69651d60caab925af9829054d107ec8b19af3082d SHA512 824eddd7db24177f7e15b90fb93a0426c2b8cee4dbcac2707f4cc7e7e42bafcad3775382b79d9b4d679e0c4b5c17a1b79ad134e91a968037336b34c6262e9c48 WHIRLPOOL 7056444822e7a0de619dcab933a7870ebe7db52008f3dbb2dd72aa189325d7ca4c353133d77150ec67c414e005a834458538f57746b13fd20f06bc7289869800 |
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DIST bowtie-1.1.2-src.zip 7713258 SHA256 b1e9ccc825207efd1893d9e33244c681bcb89b9b2b811eb95a9f5a92eab637ae SHA512 3d3d69bc3a865bb577b5a91440215d0d5b606c7a8751d565e606e36adbfbdef695b1718ae81cd3e2682a39ca7784c4d00976441e7618264ad99b04c7f53c36e8 WHIRLPOOL 08cb824bf7a1ddfbe6692de67191aacf44776d7d4e0ab66bd2a13ecfffd087bc28cdde4c7285c781fa4759de0a239e68f87b702bcc2e24c9b81fda5804360ce7 |
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DIST bowtie2-2.2.6-source.zip 5728779 SHA256 1000e90cdd90c3ca43c69d0d0ad951e190d36a6981a546f430a90ce86d64bfc8 SHA512 3ab5a5475cf214affd91e0d1782fd2d6dedccd979e3c809b5dfb272726d99ff1c7b59d92e387b187a7c2e43557786a1085186ccb96588de91212caf2eb94ce4f WHIRLPOOL 4fb02b3a0d76bbee0fe9abf91a71405922568bc38e593d5740df6279bad6f8b668df0debb0a81f3d3c23623558f34d842dd662a6838cf2d7f0fc8945fd00a298 |
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|
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diff --git a/sci-biology/bowtie/bowtie-0.12.8.ebuild b/sci-biology/bowtie/bowtie-0.12.8.ebuild |
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deleted file mode 100644 |
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index c26c986..0000000 |
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--- a/sci-biology/bowtie/bowtie-0.12.8.ebuild |
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+++ /dev/null |
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@@ -1,44 +0,0 @@ |
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-# Copyright 1999-2013 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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-# $Id$ |
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- |
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-EAPI=4 |
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- |
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-inherit eutils toolchain-funcs |
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- |
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-DESCRIPTION="An ultrafast memory-efficient short read aligner" |
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-HOMEPAGE="http://bowtie-bio.sourceforge.net/" |
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-SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" |
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- |
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-LICENSE="Artistic" |
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-SLOT="0" |
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-IUSE="" |
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-KEYWORDS="amd64 x86 ~x64-macos" |
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- |
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-DEPEND="app-arch/unzip" |
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-RDEPEND="" |
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- |
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-# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library (http://www.seqan.de) |
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-# TODO: properly report system CFLAGS in -DCOMPILE_OPTIONS |
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- |
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-src_prepare() { |
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- epatch "${FILESDIR}"/${P}-gcc-47.patch |
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-} |
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- |
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-src_compile() { |
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- unset CFLAGS |
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- emake \ |
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- CC="$(tc-getCC)" \ |
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- CPP="$(tc-getCXX)" \ |
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- CXX="$(tc-getCXX)" \ |
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- EXTRA_FLAGS="${LDFLAGS}" \ |
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- RELEASE_FLAGS="" |
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-} |
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- |
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-src_install() { |
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- dobin bowtie bowtie-* |
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- exeinto /usr/share/${PN}/scripts |
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- doexe scripts/* |
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- newman MANUAL bowtie.1 |
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- dodoc AUTHORS NEWS TUTORIAL |
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-} |
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|
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diff --git a/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch b/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch |
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deleted file mode 100644 |
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index 3c8a1e1..0000000 |
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--- a/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch |
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+++ /dev/null |
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@@ -1,45 +0,0 @@ |
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- alphabet.h | 24 ++++++++++++------------ |
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- 1 files changed, 12 insertions(+), 12 deletions(-) |
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- |
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-diff --git a/alphabet.h b/alphabet.h |
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-index b464ddf..08d0281 100644 |
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---- a/alphabet.h |
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-+++ b/alphabet.h |
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-@@ -38,6 +38,18 @@ static inline TStr reverseComplement(const TStr& s, bool color) { |
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- return s_rc; |
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- } |
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- |
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-+/// Reverse a string in-place |
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-+template <typename TStr> |
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-+static inline void reverseInPlace(TStr& s) { |
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-+ typedef typename Value<TStr>::Type TVal; |
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-+ size_t len = length(s); |
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-+ for(size_t i = 0; i < (len>>1); i++) { |
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-+ TVal tmp = s[i]; |
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-+ s[i] = s[len-i-1]; |
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-+ s[len-i-1] = tmp; |
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-+ } |
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-+} |
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-+ |
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- /** |
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- * Reverse-complement s in-place. Ns go to Ns. |
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- */ |
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-@@ -69,18 +81,6 @@ static inline void reverseComplementInPlace(TStr& s, bool color) { |
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- } |
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- } |
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- |
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--/// Reverse a string in-place |
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--template <typename TStr> |
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--static inline void reverseInPlace(TStr& s) { |
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-- typedef typename Value<TStr>::Type TVal; |
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-- size_t len = length(s); |
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-- for(size_t i = 0; i < (len>>1); i++) { |
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-- TVal tmp = s[i]; |
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-- s[i] = s[len-i-1]; |
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-- s[len-i-1] = tmp; |
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-- } |
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--} |
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-- |
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- /** |
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- * Return the reverse-complement of s. |
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- */ |