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authorJustin Lecher <jlec@gentoo.org>2015-12-26 19:02:47 +0100
committerJustin Lecher <jlec@gentoo.org>2015-12-26 19:02:47 +0100
commit369678cffc9f7ecae414f3800f01a2c2251e8669 (patch)
treebd63aa0a85e4636964e1fe5477cb1a1ee42fa064 /sci-biology
parentdev-python/pysvn: Drop vulnerable version for CVE-2015-0853 (diff)
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sci-biology/bowtie: Drop old
obsoletes: Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=564320 Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/bowtie/Manifest1
-rw-r--r--sci-biology/bowtie/bowtie-0.12.8.ebuild44
-rw-r--r--sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch45
3 files changed, 0 insertions, 90 deletions
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index c692c89b3bb..1291400caba 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,3 +1,2 @@
-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
deleted file mode 100644
index c26c986ed19..00000000000
--- a/sci-biology/bowtie/bowtie-0.12.8.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# 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
deleted file mode 100644
index 3c8a1e1d9ca..00000000000
--- a/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch
+++ /dev/null
@@ -1,45 +0,0 @@
- 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.
- */