commit: 50fe91c03b9c8431a871463ee75ae68bdfc8a171 Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com> AuthorDate: Sun Oct 11 08:04:43 2015 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Wed Oct 14 12:47:58 2015 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=50fe91c0
sci-biology/bowtie: bring back stable bowtie-0.12.8 bowtie-0.12.8 is the only stable variant and removing it breaks the stable depgraph. sci-biology/bowtie/Manifest | 1 + sci-biology/bowtie/bowtie-0.12.8.ebuild | 44 +++++++++++++++++++++ .../bowtie/files/bowtie-0.12.8-gcc-47.patch | 45 ++++++++++++++++++++++ 3 files changed, 90 insertions(+) diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest index 1291400..c692c89 100644 --- a/sci-biology/bowtie/Manifest +++ b/sci-biology/bowtie/Manifest @@ -1,2 +1,3 @@ +DIST bowtie-0.12.8-src.zip 15569919 SHA256 f074a0f25e156976c4951fd69651d60caab925af9829054d107ec8b19af3082d SHA512 824eddd7db24177f7e15b90fb93a0426c2b8cee4dbcac2707f4cc7e7e42bafcad3775382b79d9b4d679e0c4b5c17a1b79ad134e91a968037336b34c6262e9c48 WHIRLPOOL 7056444822e7a0de619dcab933a7870ebe7db52008f3dbb2dd72aa189325d7ca4c353133d77150ec67c414e005a834458538f57746b13fd20f06bc7289869800 DIST bowtie-1.1.2-src.zip 7713258 SHA256 b1e9ccc825207efd1893d9e33244c681bcb89b9b2b811eb95a9f5a92eab637ae SHA512 3d3d69bc3a865bb577b5a91440215d0d5b606c7a8751d565e606e36adbfbdef695b1718ae81cd3e2682a39ca7784c4d00976441e7618264ad99b04c7f53c36e8 WHIRLPOOL 08cb824bf7a1ddfbe6692de67191aacf44776d7d4e0ab66bd2a13ecfffd087bc28cdde4c7285c781fa4759de0a239e68f87b702bcc2e24c9b81fda5804360ce7 DIST bowtie2-2.2.6-source.zip 5728779 SHA256 1000e90cdd90c3ca43c69d0d0ad951e190d36a6981a546f430a90ce86d64bfc8 SHA512 3ab5a5475cf214affd91e0d1782fd2d6dedccd979e3c809b5dfb272726d99ff1c7b59d92e387b187a7c2e43557786a1085186ccb96588de91212caf2eb94ce4f WHIRLPOOL 4fb02b3a0d76bbee0fe9abf91a71405922568bc38e593d5740df6279bad6f8b668df0debb0a81f3d3c23623558f34d842dd662a6838cf2d7f0fc8945fd00a298 diff --git a/sci-biology/bowtie/bowtie-0.12.8.ebuild b/sci-biology/bowtie/bowtie-0.12.8.ebuild new file mode 100644 index 0000000..c26c986 --- /dev/null +++ b/sci-biology/bowtie/bowtie-0.12.8.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="An ultrafast memory-efficient short read aligner" +HOMEPAGE="http://bowtie-bio.sourceforge.net/"; +SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" + +LICENSE="Artistic" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86 ~x64-macos" + +DEPEND="app-arch/unzip" +RDEPEND="" + +# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library (http://www.seqan.de) +# TODO: properly report system CFLAGS in -DCOMPILE_OPTIONS + +src_prepare() { + epatch "${FILESDIR}"/${P}-gcc-47.patch +} + +src_compile() { + unset CFLAGS + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CXX="$(tc-getCXX)" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="" +} + +src_install() { + dobin bowtie bowtie-* + exeinto /usr/share/${PN}/scripts + doexe scripts/* + newman MANUAL bowtie.1 + dodoc AUTHORS NEWS TUTORIAL +} 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 new file mode 100644 index 0000000..3c8a1e1 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch @@ -0,0 +1,45 @@ + alphabet.h | 24 ++++++++++++------------ + 1 files changed, 12 insertions(+), 12 deletions(-) + +diff --git a/alphabet.h b/alphabet.h +index b464ddf..08d0281 100644 +--- a/alphabet.h ++++ b/alphabet.h +@@ -38,6 +38,18 @@ static inline TStr reverseComplement(const TStr& s, bool color) { + return s_rc; + } + ++/// Reverse a string in-place ++template <typename TStr> ++static inline void reverseInPlace(TStr& s) { ++ typedef typename Value<TStr>::Type TVal; ++ size_t len = length(s); ++ for(size_t i = 0; i < (len>>1); i++) { ++ TVal tmp = s[i]; ++ s[i] = s[len-i-1]; ++ s[len-i-1] = tmp; ++ } ++} ++ + /** + * Reverse-complement s in-place. Ns go to Ns. + */ +@@ -69,18 +81,6 @@ static inline void reverseComplementInPlace(TStr& s, bool color) { + } + } + +-/// Reverse a string in-place +-template <typename TStr> +-static inline void reverseInPlace(TStr& s) { +- typedef typename Value<TStr>::Type TVal; +- size_t len = length(s); +- for(size_t i = 0; i < (len>>1); i++) { +- TVal tmp = s[i]; +- s[i] = s[len-i-1]; +- s[len-i-1] = tmp; +- } +-} +- + /** + * Return the reverse-complement of s. + */
