[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
commit: 9de8c676fe59c8570f2982846b440973beb8cafd
Author: Pacho Ramos gentoo org>
AuthorDate: Tue Jul 30 19:40:05 2024 +
Commit: Pacho Ramos gentoo org>
CommitDate: Tue Jul 30 21:11:51 2024 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9de8c676
sci-biology/bowtie: enable py3.12
Closes: https://bugs.gentoo.org/929753
Signed-off-by: Pacho Ramos gentoo.org>
sci-biology/bowtie/bowtie-2.5.1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/bowtie/bowtie-2.5.1.ebuild
b/sci-biology/bowtie/bowtie-2.5.1.ebuild
index b30a2b920f4e..a2b75d6b9880 100644
--- a/sci-biology/bowtie/bowtie-2.5.1.ebuild
+++ b/sci-biology/bowtie/bowtie-2.5.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
inherit python-single-r1 toolchain-funcs
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
commit: ad0f0da9f1b0df76d06b2bd4c52ce233ce4c8001
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Fri Feb 24 07:29:55 2023 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Fri Feb 24 07:29:55 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ad0f0da9
sci-biology/bowtie: add 2.5.1
Signed-off-by: Andrew Ammerlaan gentoo.org>
sci-biology/bowtie/Manifest| 1 +
sci-biology/bowtie/bowtie-2.5.1.ebuild | 73 ++
2 files changed, 74 insertions(+)
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index e62703395825..274e5e7b9fb6 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1 +1,2 @@
DIST bowtie2-2.4.4-source.zip 10515984 BLAKE2B
be4ceb9d3155d2a9a1f580e5032251b04b89ce0c8c9c89fc3551b34fe3bd71a683362488be7aad6daef24734c6f95c19223f20e67f198f745c4432381243039c
SHA512
1b5dadd7e41b90bb9b05f50bfa171fe219cfd03aa8bb6f800de4baaffeb975eef6efc4fb8b49cb0d18833f74a1741cbe1556b87388f59188e04a55dcee6a02da
+DIST bowtie2-2.5.1-source.zip 10528859 BLAKE2B
9dc22bfef4b3a1cfaa606cb235acd1d7688015678d82e8ca80d3d7cf269e1f45d6cb60bc29eb334fb6f0c25d5afd8202e83a83e53668c8965857b8885d2692c8
SHA512
31cc642e318ab50e7ef6035a9c2095024d46d92a317011ed0c3ac3ccb3d427a13bf724d0158d29a4f1e07115ddcb85229b95bcb2d4351164fcadd6568293565f
diff --git a/sci-biology/bowtie/bowtie-2.5.1.ebuild
b/sci-biology/bowtie/bowtie-2.5.1.ebuild
new file mode 100644
index ..353362fd6026
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-2.5.1.ebuild
@@ -0,0 +1,73 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..11} )
+
+inherit python-single-r1 toolchain-funcs
+
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
+HOMEPAGE="https://bowtie-bio.sourceforge.net/bowtie2/";
+SRC_URI="mirror://sourceforge/project/${PN}-bio/bowtie2/${PV}/bowtie2-${PV}-source.zip"
+S="${WORKDIR}/${PN}2-${PV}"
+
+LICENSE="GPL-3"
+SLOT="2"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="test cpu_flags_x86_sse2 examples"
+# Test script missing from tarball
+# ./scripts/sim/run.sh: No such file or directory
+RESTRICT="test"
+REQUIRED_USE="cpu_flags_x86_sse2 ${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+ ${PYTHON_DEPS}
+ dev-lang/perl
+ sys-libs/zlib
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ app-arch/unzip
+ test? (
+ dev-perl/App-cpanminus
+ dev-perl/B-COW
+ dev-perl/Clone
+ dev-perl/Config-General
+ dev-perl/File-Which
+ dev-perl/local-lib
+ dev-perl/Math-Random
+ dev-perl/Test-Deep
+ dev-perl/Text-Template
+ )
+"
+
+src_compile() {
+ emake \
+ CXX="$(tc-getCXX)" \
+ CXXFLAGS="" \
+ CPPFLAGS="${CPPFLAGS}" \
+ EXTRA_FLAGS="${LDFLAGS}" \
+ RELEASE_FLAGS="${CXXFLAGS} -msse2"
+}
+
+src_install() {
+ dobin bowtie2 bowtie2-*
+
+ exeinto /usr/libexec/bowtie2
+ doexe scripts/*
+
+ HTML_DOCS=( doc/{manual.html,style.css} )
+ einstalldocs
+ dodoc TUTORIAL
+ newman MANUAL bowtie2.1
+
+ python_fix_shebang "${ED}"/usr/bin/bowtie2-{build,inspect}
+
+ if use examples; then
+ docinto examples
+ dodoc -r example/.
+ docompress -x /usr/share/doc/${PF}/examples
+ fi
+}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
commit: e99b33b0d98ad381a2a4ceaab86f86dd5e2d2d00
Author: David Seifert gentoo org>
AuthorDate: Sun Aug 1 17:02:01 2021 +
Commit: David Seifert gentoo org>
CommitDate: Sun Aug 1 17:02:01 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e99b33b0
sci-biology/bowtie: fix QA issues
Signed-off-by: David Seifert gentoo.org>
sci-biology/bowtie/bowtie-2.4.4.ebuild | 2 +-
sci-biology/bowtie/metadata.xml| 19 +++
2 files changed, 8 insertions(+), 13 deletions(-)
diff --git a/sci-biology/bowtie/bowtie-2.4.4.ebuild
b/sci-biology/bowtie/bowtie-2.4.4.ebuild
index 6621b5babd9..2ba75bc2bca 100644
--- a/sci-biology/bowtie/bowtie-2.4.4.ebuild
+++ b/sci-biology/bowtie/bowtie-2.4.4.ebuild
@@ -16,7 +16,7 @@ LICENSE="GPL-3"
SLOT="2"
KEYWORDS="~amd64 ~x86"
IUSE="cpu_flags_x86_sse2 examples"
-REQUIRED_USE="cpu_flags_x86_sse2"
+REQUIRED_USE="cpu_flags_x86_sse2 ${PYTHON_REQUIRED_USE}"
RDEPEND="
${PYTHON_DEPS}
diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml
index 71e8d3bb8e0..f570878c86e 100644
--- a/sci-biology/bowtie/metadata.xml
+++ b/sci-biology/bowtie/metadata.xml
@@ -1,16 +1,11 @@
http://www.gentoo.org/dtd/metadata.dtd";>
-
-sci-biol...@gentoo.org
-Gentoo Biology Project
-
-
-bowtie-bio
-
-
-Enables building bowtie with the Intel
- Threading Building Blocks from dev-cpp/tbb. This
- flag is recommended.
-
+
+ sci-biol...@gentoo.org
+ Gentoo Biology Project
+
+
+ bowtie-bio
+
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
commit: b3c6b97c03059d44b801c71c3ccf7a6165593149
Author: David Seifert gentoo org>
AuthorDate: Sun Aug 1 16:40:42 2021 +
Commit: David Seifert gentoo org>
CommitDate: Sun Aug 1 16:40:42 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b3c6b97c
sci-biology/bowtie: drop 2.2.9
Closes: https://bugs.gentoo.org/722870
Signed-off-by: David Seifert gentoo.org>
sci-biology/bowtie/Manifest| 1 -
sci-biology/bowtie/bowtie-2.2.9.ebuild | 61 --
.../bowtie/files/bowtie-2.2.9-fix-c++14.patch | 29 --
3 files changed, 91 deletions(-)
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index 96d35e2bfd2..e6270339582 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,2 +1 @@
-DIST bowtie2-2.2.9-source.zip 5734235 BLAKE2B
ec48e09fe05403d1085bb4e0c6ef1325b8912da0a8c942061c34f3381c6dd7ccdcc64c4bcdbb18c1da84ac57e1e34cc866fe79809c33c2769a8d75ecde7d0846
SHA512
ead8f7641f3231638d986f9e500bc4ec7afe1e542048465bfcc2e93e2b2d2e499f0dd8aa5c1e3e21df285c9d195b187682eb7e12be4a408f6c50fb97c0e0a205
DIST bowtie2-2.4.4-source.zip 10515984 BLAKE2B
be4ceb9d3155d2a9a1f580e5032251b04b89ce0c8c9c89fc3551b34fe3bd71a683362488be7aad6daef24734c6f95c19223f20e67f198f745c4432381243039c
SHA512
1b5dadd7e41b90bb9b05f50bfa171fe219cfd03aa8bb6f800de4baaffeb975eef6efc4fb8b49cb0d18833f74a1741cbe1556b87388f59188e04a55dcee6a02da
diff --git a/sci-biology/bowtie/bowtie-2.2.9.ebuild
b/sci-biology/bowtie/bowtie-2.2.9.ebuild
deleted file mode 100644
index 0bacb8ca25d..000
--- a/sci-biology/bowtie/bowtie-2.2.9.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/";
-SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
-
-LICENSE="GPL-3"
-SLOT="2"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="examples cpu_flags_x86_sse2 +tbb"
-
-RDEPEND="dev-lang/perl
- tbb? ( dev-cpp/tbb )"
-DEPEND="${RDEPEND}
- app-arch/unzip"
-
-S="${WORKDIR}/${PN}2-${PV}"
-
-DOCS=( AUTHORS NEWS TUTORIAL )
-HTML_DOCS=( doc/{manual.html,style.css} )
-PATCHES=( "${FILESDIR}/${PN}-2.2.9-fix-c++14.patch" )
-
-pkg_pretend() {
- if ! use cpu_flags_x86_sse2 ; then
- eerror "This package requires a CPU supporting the SSE2
instruction set."
- die "SSE2 support missing"
- fi
-}
-
-src_compile() {
- emake \
- CC="$(tc-getCC)" \
- CPP="$(tc-getCXX)" \
- CXX="$(tc-getCXX)" \
- CFLAGS="" \
- CXXFLAGS="" \
- EXTRA_FLAGS="${LDFLAGS}" \
- RELEASE_FLAGS="${CXXFLAGS} -msse2" \
- WITH_TBB="$(usex tbb 1 0)"
-}
-
-src_install() {
- dobin ${PN}2 ${PN}2-*
-
- exeinto /usr/libexec/${PN}2
- doexe scripts/*
-
- newman MANUAL ${PN}2.1
- einstalldocs
-
- if use examples; then
- insinto /usr/share/${PN}2
- doins -r example
- fi
-}
diff --git a/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch
b/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch
deleted file mode 100644
index cd2a67b6a52..000
--- a/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-Fix building with C++14, which errors out due to differing semantics between
C++98
-and C++14 with regards to allowing destructors to throw exceptions.
-See also: https://bugs.gentoo.org/show_bug.cgi?id=593966
-
a/blockwise_sa.h
-+++ b/blockwise_sa.h
-@@ -87,7 +87,11 @@
- _logger(__logger)
- { }
-
-- virtual ~BlockwiseSA() { }
-+ virtual ~BlockwiseSA()
-+#if __cplusplus >= 201103L
-+ noexcept(false)
-+#endif
-+ { }
-
- /**
-* Get the next suffix; compute the next bucket if necessary.
-@@ -216,6 +220,9 @@
- { _randomSrc.init(__seed); reset(); }
-
- ~KarkkainenBlockwiseSA()
-+#if __cplusplus >= 201103L
-+noexcept(false)
-+#endif
- {
- #ifdef WITH_TBB
- tbb_grp.wait();
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
commit: 20633430c439732edc1dd09d5b76acefcaa54c9d
Author: David Seifert gentoo org>
AuthorDate: Sun Aug 1 16:40:40 2021 +
Commit: David Seifert gentoo org>
CommitDate: Sun Aug 1 16:40:40 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=20633430
sci-biology/bowtie: add 2.4.4
Bug: https://bugs.gentoo.org/722870
Signed-off-by: David Seifert gentoo.org>
sci-biology/bowtie/Manifest| 1 +
sci-biology/bowtie/bowtie-2.4.4.ebuild | 55 ++
2 files changed, 56 insertions(+)
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index 50ad9715e98..96d35e2bfd2 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1 +1,2 @@
DIST bowtie2-2.2.9-source.zip 5734235 BLAKE2B
ec48e09fe05403d1085bb4e0c6ef1325b8912da0a8c942061c34f3381c6dd7ccdcc64c4bcdbb18c1da84ac57e1e34cc866fe79809c33c2769a8d75ecde7d0846
SHA512
ead8f7641f3231638d986f9e500bc4ec7afe1e542048465bfcc2e93e2b2d2e499f0dd8aa5c1e3e21df285c9d195b187682eb7e12be4a408f6c50fb97c0e0a205
+DIST bowtie2-2.4.4-source.zip 10515984 BLAKE2B
be4ceb9d3155d2a9a1f580e5032251b04b89ce0c8c9c89fc3551b34fe3bd71a683362488be7aad6daef24734c6f95c19223f20e67f198f745c4432381243039c
SHA512
1b5dadd7e41b90bb9b05f50bfa171fe219cfd03aa8bb6f800de4baaffeb975eef6efc4fb8b49cb0d18833f74a1741cbe1556b87388f59188e04a55dcee6a02da
diff --git a/sci-biology/bowtie/bowtie-2.4.4.ebuild
b/sci-biology/bowtie/bowtie-2.4.4.ebuild
new file mode 100644
index 000..6621b5babd9
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-2.4.4.ebuild
@@ -0,0 +1,55 @@
+# Copyright 2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit python-single-r1 toolchain-funcs
+
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/";
+SRC_URI="mirror://sourceforge/project/${PN}-bio/bowtie2/${PV}/bowtie2-${PV}-source.zip"
+S="${WORKDIR}/${PN}2-${PV}"
+
+LICENSE="GPL-3"
+SLOT="2"
+KEYWORDS="~amd64 ~x86"
+IUSE="cpu_flags_x86_sse2 examples"
+REQUIRED_USE="cpu_flags_x86_sse2"
+
+RDEPEND="
+ ${PYTHON_DEPS}
+ dev-lang/perl
+ sys-libs/zlib"
+DEPEND="${RDEPEND}"
+BDEPEND="app-arch/unzip"
+
+src_compile() {
+ emake \
+ CXX="$(tc-getCXX)" \
+ CXXFLAGS="" \
+ CPPFLAGS="${CPPFLAGS}" \
+ EXTRA_FLAGS="${LDFLAGS}" \
+ RELEASE_FLAGS="${CXXFLAGS} -msse2"
+}
+
+src_install() {
+ dobin bowtie2 bowtie2-*
+
+ exeinto /usr/libexec/bowtie2
+ doexe scripts/*
+
+ HTML_DOCS=( doc/{manual.html,style.css} )
+ einstalldocs
+ dodoc TUTORIAL
+ newman MANUAL bowtie2.1
+
+ python_fix_shebang "${ED}"/usr/bin/bowtie2-{build,inspect}
+
+ if use examples; then
+ docinto examples
+ dodoc -r example/.
+ docompress -x /usr/share/doc/${PF}/examples
+ fi
+}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/
commit: 72b619bb3a27ec63f571afbf73ec75893fcc2d99
Author: Michał Górny gentoo org>
AuthorDate: Wed Sep 9 10:26:34 2020 +
Commit: Michał Górny gentoo org>
CommitDate: Wed Sep 9 10:34:29 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=72b619bb
sci-biology/bowtie: Remove old
Signed-off-by: Michał Górny gentoo.org>
sci-biology/bowtie/Manifest| 1 -
sci-biology/bowtie/bowtie-1.1.2-r1.ebuild | 74
.../files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch | 17 -
.../files/bowtie-1.1.2-fix-setBegin-call.patch | 42 ---
.../bowtie/files/bowtie-1.1.2-seqan-popcount.patch | 24 --
.../bowtie-1.1.2-seqan-rename-ChunkPool.patch | 382 -
.../bowtie-1.1.2-seqan-rename-fill-to-resize.patch | 85 -
.../bowtie/files/bowtie-1.1.2-spelling.patch | 48 ---
.../bowtie-1.1.2-tbb-tinythread-missing.patch | 18 -
.../bowtie/files/bowtie-1.1.2-unbundle-seqan.patch | 27 --
10 files changed, 718 deletions(-)
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index 824c7439adc..50ad9715e98 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,2 +1 @@
-DIST bowtie-1.1.2-src.zip 7713258 BLAKE2B
ac10aca905099b5a70d3fab6f90e2dc4713bf7b460d027abf89a6ef6103979724e70b2915a86ffa571b59dcd9df768c80be1846cccd08f7f85dd402ce64c0cb0
SHA512
3d3d69bc3a865bb577b5a91440215d0d5b606c7a8751d565e606e36adbfbdef695b1718ae81cd3e2682a39ca7784c4d00976441e7618264ad99b04c7f53c36e8
DIST bowtie2-2.2.9-source.zip 5734235 BLAKE2B
ec48e09fe05403d1085bb4e0c6ef1325b8912da0a8c942061c34f3381c6dd7ccdcc64c4bcdbb18c1da84ac57e1e34cc866fe79809c33c2769a8d75ecde7d0846
SHA512
ead8f7641f3231638d986f9e500bc4ec7afe1e542048465bfcc2e93e2b2d2e499f0dd8aa5c1e3e21df285c9d195b187682eb7e12be4a408f6c50fb97c0e0a205
diff --git a/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild
b/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild
deleted file mode 100644
index d8b607f870f..000
--- a/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit flag-o-matic toolchain-funcs
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/";
-SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
-
-LICENSE="Artistic"
-SLOT="1"
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-IUSE="examples +tbb"
-
-RDEPEND="tbb? ( dev-cpp/tbb )"
-DEPEND="${RDEPEND}
- sci-biology/seqan:1.4
- app-arch/unzip"
-
-DOCS=( AUTHORS NEWS TUTORIAL doc/README )
-HTML_DOCS=( doc/{manual.html,style.css} )
-
-PATCHES=(
- "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch"
- "${FILESDIR}/${P}-fix-setBegin-call.patch"
- "${FILESDIR}/${P}-seqan-popcount.patch"
- "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch"
- "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch"
- "${FILESDIR}/${P}-spelling.patch"
- "${FILESDIR}/${P}-tbb-tinythread-missing.patch"
- "${FILESDIR}/${P}-unbundle-seqan.patch"
-)
-
-src_prepare() {
- default
-
- # remove bundled libraries, use system seqan 1.4
- rm -rf SeqAn-1.1/ third_party/ || die
-
- # innocuous non-security flags, prevent log pollution
- append-cxxflags \
- -Wno-unused-local-typedefs \
- -Wno-unused-but-set-variable \
- -Wno-unused-variable
-}
-
-src_compile() {
- emake \
- CC="$(tc-getCC)" \
- CPP="$(tc-getCXX)" \
- CFLAGS="" \
- CXXFLAGS="" \
- EXTRA_FLAGS="${LDFLAGS}" \
- RELEASE_FLAGS="${CXXFLAGS}" \
- WITH_TBB="$(usex tbb 1 0)"
-}
-
-src_install() {
- dobin ${PN} ${PN}-*
-
- exeinto /usr/libexec/${PN}
- doexe scripts/*
-
- newman MANUAL ${PN}.1
- einstalldocs
-
- if use examples; then
- insinto /usr/share/${PN}
- doins -r genomes indexes
- fi
-}
diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch
b/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch
deleted file mode 100644
index 78b9c01a046..000
--- a/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-Description: Change class name of _Context_LSS
- New version 1.4 of SeQan uses a different name of the class.
-Forwarded: no
-Author: Gert Wollny
-Last-Update: 2014-100-06
-
a/diff_sample.h
-+++ b/diff_sample.h
-@@ -856,7 +856,7 @@ void DifferenceCoverSample::build(
- {
- Timer timer(cout, " Invoking Larsson-Sadakane on ranks time:
", this->verbose());
- VMSG_NL(" Invoking Larsson-Sadakane on ranks");
-- _Context_LSS c;
-+ ContextLss_ c;
- c.suffixsort(
- (TIndexOff*)begin(_isaPrime,
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
commit: 6d8d74d327137358ffb5e4dad142b9c8b280f71c
Author: David Seifert gentoo org>
AuthorDate: Mon Dec 25 09:57:08 2017 +
Commit: David Seifert gentoo org>
CommitDate: Mon Dec 25 16:08:50 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6d8d74d3
sci-biology/bowtie: Remove old
Closes: https://bugs.gentoo.org/630140
Package-Manager: Portage-2.3.19, Repoman-2.3.6
Closes: https://github.com/gentoo/gentoo/pull/6626
sci-biology/bowtie/Manifest| 1 -
sci-biology/bowtie/bowtie-1.1.2.ebuild | 54 --
sci-biology/bowtie/bowtie-2.2.6.ebuild | 60 --
3 files changed, 115 deletions(-)
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index 77c55873995..824c7439adc 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,3 +1,2 @@
DIST bowtie-1.1.2-src.zip 7713258 BLAKE2B
ac10aca905099b5a70d3fab6f90e2dc4713bf7b460d027abf89a6ef6103979724e70b2915a86ffa571b59dcd9df768c80be1846cccd08f7f85dd402ce64c0cb0
SHA512
3d3d69bc3a865bb577b5a91440215d0d5b606c7a8751d565e606e36adbfbdef695b1718ae81cd3e2682a39ca7784c4d00976441e7618264ad99b04c7f53c36e8
-DIST bowtie2-2.2.6-source.zip 5728779 BLAKE2B
acd821376755e6bebfd58c39012a370b1aadf4cf8c52eafa1c648c93a0cab695c9c37761498260ed709bc25eb0b671797ff1c74da9787d616c8c39d1296a37eb
SHA512
3ab5a5475cf214affd91e0d1782fd2d6dedccd979e3c809b5dfb272726d99ff1c7b59d92e387b187a7c2e43557786a1085186ccb96588de91212caf2eb94ce4f
DIST bowtie2-2.2.9-source.zip 5734235 BLAKE2B
ec48e09fe05403d1085bb4e0c6ef1325b8912da0a8c942061c34f3381c6dd7ccdcc64c4bcdbb18c1da84ac57e1e34cc866fe79809c33c2769a8d75ecde7d0846
SHA512
ead8f7641f3231638d986f9e500bc4ec7afe1e542048465bfcc2e93e2b2d2e499f0dd8aa5c1e3e21df285c9d195b187682eb7e12be4a408f6c50fb97c0e0a205
diff --git a/sci-biology/bowtie/bowtie-1.1.2.ebuild
b/sci-biology/bowtie/bowtie-1.1.2.ebuild
deleted file mode 100644
index 1ada8a0fdc2..000
--- a/sci-biology/bowtie/bowtie-1.1.2.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/";
-SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
-
-LICENSE="Artistic"
-SLOT="1"
-KEYWORDS="amd64 x86 ~x64-macos"
-
-IUSE="examples +tbb"
-
-DEPEND="app-arch/unzip
- tbb? ( dev-cpp/tbb )"
-RDEPEND=""
-
-DOCS=( AUTHORS NEWS TUTORIAL doc/README )
-HTML_DOCS=( doc/{manual.html,style.css} )
-
-src_prepare() {
- # always include tinythread.cpp
- epatch "${FILESDIR}/${P}-tbb-tinythread-missing.patch"
-}
-
-src_compile() {
- emake \
- CC="$(tc-getCC)" \
- CPP="$(tc-getCXX)" \
- CFLAGS="" \
- CXXFLAGS="" \
- EXTRA_FLAGS="${LDFLAGS}" \
- RELEASE_FLAGS="${CXXFLAGS}" \
- WITH_TBB="$(usex tbb 1 0)"
-}
-
-src_install() {
- dobin ${PN} ${PN}-*
-
- exeinto /usr/libexec/${PN}
- doexe scripts/*
-
- newman MANUAL ${PN}.1
- einstalldocs
-
- if use examples; then
- insinto /usr/share/${PN}
- doins -r genomes indexes
- fi
-}
diff --git a/sci-biology/bowtie/bowtie-2.2.6.ebuild
b/sci-biology/bowtie/bowtie-2.2.6.ebuild
deleted file mode 100644
index 29826473a3b..000
--- a/sci-biology/bowtie/bowtie-2.2.6.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/";
-SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
-
-LICENSE="GPL-3"
-SLOT="2"
-KEYWORDS="amd64 x86"
-
-IUSE="examples cpu_flags_x86_sse2 +tbb"
-
-RDEPEND="dev-lang/perl"
-DEPEND="${RDEPEND}
- app-arch/unzip
- tbb? ( dev-cpp/tbb )"
-
-S="${WORKDIR}/${PN}2-${PV}"
-
-DOCS=( AUTHORS NEWS TUTORIAL )
-HTML_DOCS=( doc/{manual.html,style.css} )
-
-pkg_pretend() {
- if ! use cpu_flags_x86_sse2 ; then
- eerror "This package requires a CPU supporting the SSE2
instruction set."
- die "SSE2 support missing"
- fi
-}
-
-src_compile() {
- emake \
- CC="$(tc-getCC)" \
- CPP="$(tc-getCXX)" \
- CXX="$(tc-getCXX)" \
- CFLAGS="" \
- CXXFLAGS="" \
- EXTRA_FLAGS="${LDFLAGS}" \
- RELEASE_FLAGS="${CXXFLAGS} -msse2" \
- WITH_TBB="$(usex tbb 1 0)"
-}
-
-src_install() {
- dobin ${PN}2 ${PN}2-*
-
- exeinto /usr/libexec/${PN}2
- doexe scripts/*
-
- newman MANUAL ${PN}2.1
- einstalldocs
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
commit: a4da0209640e967dbbc8cd85820ff8858e34f872
Author: David Seifert gentoo org>
AuthorDate: Sun Sep 18 22:39:18 2016 +
Commit: David Seifert gentoo org>
CommitDate: Sun Sep 18 22:39:56 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a4da0209
sci-biology/bowtie: Allow for compiling with GCC 6
Gentoo-bug: 593966
Package-Manager: portage-2.3.0
sci-biology/bowtie/bowtie-2.2.9.ebuild | 3 ++-
.../bowtie/files/bowtie-2.2.9-fix-c++14.patch | 29 ++
2 files changed, 31 insertions(+), 1 deletion(-)
diff --git a/sci-biology/bowtie/bowtie-2.2.9.ebuild
b/sci-biology/bowtie/bowtie-2.2.9.ebuild
index 6e66420..8544512 100644
--- a/sci-biology/bowtie/bowtie-2.2.9.ebuild
+++ b/sci-biology/bowtie/bowtie-2.2.9.ebuild
@@ -4,7 +4,7 @@
EAPI=6
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/";
@@ -25,6 +25,7 @@ S="${WORKDIR}/${PN}2-${PV}"
DOCS=( AUTHORS NEWS TUTORIAL )
HTML_DOCS=( doc/{manual.html,style.css} )
+PATCHES=( "${FILESDIR}/${PN}-2.2.9-fix-c++14.patch" )
pkg_pretend() {
if ! use cpu_flags_x86_sse2 ; then
diff --git a/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch
b/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch
new file mode 100644
index ..cd2a67b
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch
@@ -0,0 +1,29 @@
+Fix building with C++14, which errors out due to differing semantics between
C++98
+and C++14 with regards to allowing destructors to throw exceptions.
+See also: https://bugs.gentoo.org/show_bug.cgi?id=593966
+
+--- a/blockwise_sa.h
b/blockwise_sa.h
+@@ -87,7 +87,11 @@
+ _logger(__logger)
+ { }
+
+- virtual ~BlockwiseSA() { }
++ virtual ~BlockwiseSA()
++#if __cplusplus >= 201103L
++ noexcept(false)
++#endif
++ { }
+
+ /**
+* Get the next suffix; compute the next bucket if necessary.
+@@ -216,6 +220,9 @@
+ { _randomSrc.init(__seed); reset(); }
+
+ ~KarkkainenBlockwiseSA()
++#if __cplusplus >= 201103L
++noexcept(false)
++#endif
+ {
+ #ifdef WITH_TBB
+ tbb_grp.wait();
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
commit: adf47f7e0b7623ad7740c8226b95a69f978072ba
Author: David Seifert gentoo org>
AuthorDate: Sat Jun 4 21:17:19 2016 +
Commit: David Seifert gentoo org>
CommitDate: Sat Jun 4 21:17:33 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=adf47f7e
sci-biology/bowtie: version bump
Package-Manager: portage-2.3.0_rc1
sci-biology/bowtie/Manifest | 2 +-
sci-biology/bowtie/{bowtie-2.2.8.ebuild => bowtie-2.2.9.ebuild} | 0
2 files changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index c41c821..0d7cf9c 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,3 +1,3 @@
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
-DIST bowtie2-2.2.8-source.zip 5734037 SHA256
4a36edf62c761082da1f7e7fcf363ec4ce022bd5e7c76dd3ab63fa6f0137c05b SHA512
be059498a6cb0d422b4cb0734c2067e55c66659d1e708c540d937aa52c967fc13081757fb44b8d42967b44ac6768fb00ad31fac63d69d09f2dcfd49cf4cffd62
WHIRLPOOL
6e980cc4b09280894572ffe5897387d8b414bb190a77fa53ecbae168a40dcc23afa2eee34da043e77c8e8c2d00b2da562c7d5d4a3dd7e440f8b88655b6fe56cb
+DIST bowtie2-2.2.9-source.zip 5734235 SHA256
35b3cd8efc4c1c1efac6d94e626183bf4f8608b3a745fedd294c8fba46308201 SHA512
ead8f7641f3231638d986f9e500bc4ec7afe1e542048465bfcc2e93e2b2d2e499f0dd8aa5c1e3e21df285c9d195b187682eb7e12be4a408f6c50fb97c0e0a205
WHIRLPOOL
ed8894096997ddd724c871a82b14bfa8149a23c040463c6f347ddce070a8c44baeb21bc1adc41a756e0e02c8f4861b967477c2f3469a71ca58b7d3e60aac
diff --git a/sci-biology/bowtie/bowtie-2.2.8.ebuild
b/sci-biology/bowtie/bowtie-2.2.9.ebuild
similarity index 100%
rename from sci-biology/bowtie/bowtie-2.2.8.ebuild
rename to sci-biology/bowtie/bowtie-2.2.9.ebuild
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
commit: c9b8497a77f3a72c025ca02d8fd8bdb024e34189
Author: David Seifert gentoo org>
AuthorDate: Sun Apr 10 09:47:56 2016 +
Commit: David Seifert gentoo org>
CommitDate: Sun Apr 10 09:48:08 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c9b8497a
sci-biology/bowtie: Version bump to 2.2.8
* EAPI=6
Package-Manager: portage-2.2.28
sci-biology/bowtie/Manifest| 1 +
sci-biology/bowtie/bowtie-2.2.8.ebuild | 61 ++
2 files changed, 62 insertions(+)
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index 1291400..c41c821 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,2 +1,3 @@
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
+DIST bowtie2-2.2.8-source.zip 5734037 SHA256
4a36edf62c761082da1f7e7fcf363ec4ce022bd5e7c76dd3ab63fa6f0137c05b SHA512
be059498a6cb0d422b4cb0734c2067e55c66659d1e708c540d937aa52c967fc13081757fb44b8d42967b44ac6768fb00ad31fac63d69d09f2dcfd49cf4cffd62
WHIRLPOOL
6e980cc4b09280894572ffe5897387d8b414bb190a77fa53ecbae168a40dcc23afa2eee34da043e77c8e8c2d00b2da562c7d5d4a3dd7e440f8b88655b6fe56cb
diff --git a/sci-biology/bowtie/bowtie-2.2.8.ebuild
b/sci-biology/bowtie/bowtie-2.2.8.ebuild
new file mode 100644
index 000..6e66420
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-2.2.8.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/";
+SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
+
+LICENSE="GPL-3"
+SLOT="2"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="examples cpu_flags_x86_sse2 +tbb"
+
+RDEPEND="dev-lang/perl
+ tbb? ( dev-cpp/tbb )"
+DEPEND="${RDEPEND}
+ app-arch/unzip"
+
+S="${WORKDIR}/${PN}2-${PV}"
+
+DOCS=( AUTHORS NEWS TUTORIAL )
+HTML_DOCS=( doc/{manual.html,style.css} )
+
+pkg_pretend() {
+ if ! use cpu_flags_x86_sse2 ; then
+ eerror "This package requires a CPU supporting the SSE2
instruction set."
+ die "SSE2 support missing"
+ fi
+}
+
+src_compile() {
+ emake \
+ CC="$(tc-getCC)" \
+ CPP="$(tc-getCXX)" \
+ CXX="$(tc-getCXX)" \
+ CFLAGS="" \
+ CXXFLAGS="" \
+ EXTRA_FLAGS="${LDFLAGS}" \
+ RELEASE_FLAGS="${CXXFLAGS} -msse2" \
+ WITH_TBB="$(usex tbb 1 0)"
+}
+
+src_install() {
+ dobin ${PN}2 ${PN}2-*
+
+ exeinto /usr/libexec/${PN}2
+ doexe scripts/*
+
+ newman MANUAL ${PN}2.1
+ einstalldocs
+
+ if use examples; then
+ insinto /usr/share/${PN}2
+ doins -r example
+ fi
+}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
commit: 1e3f5d88f730c5d04b64095114d2e48c1ec4ba58
Author: David Seifert gentoo org>
AuthorDate: Sat Apr 9 18:26:28 2016 +
Commit: David Seifert gentoo org>
CommitDate: Sat Apr 9 18:57:05 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1e3f5d88
sci-biology/bowtie: unbundle SeqAn, import Debian patches
* EAPI=6
Package-Manager: portage-2.2.28
sci-biology/bowtie/bowtie-1.1.2-r1.ebuild | 75
.../files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch | 17 +
.../files/bowtie-1.1.2-fix-setBegin-call.patch | 42 +++
.../bowtie/files/bowtie-1.1.2-seqan-popcount.patch | 24 ++
.../bowtie-1.1.2-seqan-rename-ChunkPool.patch | 382 +
.../bowtie-1.1.2-seqan-rename-fill-to-resize.patch | 85 +
.../bowtie/files/bowtie-1.1.2-spelling.patch | 48 +++
.../bowtie/files/bowtie-1.1.2-unbundle-seqan.patch | 27 ++
8 files changed, 700 insertions(+)
diff --git a/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild
b/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild
new file mode 100644
index 000..e0b4358
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild
@@ -0,0 +1,75 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit flag-o-matic toolchain-funcs
+
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/";
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
+
+LICENSE="Artistic"
+SLOT="1"
+KEYWORDS="~amd64 ~x86 ~x64-macos"
+
+IUSE="examples +tbb"
+
+RDEPEND="tbb? ( dev-cpp/tbb )"
+DEPEND="${RDEPEND}
+ sci-biology/seqan:1.4
+ app-arch/unzip"
+
+DOCS=( AUTHORS NEWS TUTORIAL doc/README )
+HTML_DOCS=( doc/{manual.html,style.css} )
+
+PATCHES=(
+ "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch"
+ "${FILESDIR}/${P}-fix-setBegin-call.patch"
+ "${FILESDIR}/${P}-seqan-popcount.patch"
+ "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch"
+ "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch"
+ "${FILESDIR}/${P}-spelling.patch"
+ "${FILESDIR}/${P}-tbb-tinythread-missing.patch"
+ "${FILESDIR}/${P}-unbundle-seqan.patch"
+)
+
+src_prepare() {
+ default
+
+ # remove bundled libraries, use system seqan 1.4
+ rm -rf SeqAn-1.1/ third_party/ || die
+
+ # innocuous non-security flags, prevent log pollution
+ append-cxxflags \
+ -Wno-unused-local-typedefs \
+ -Wno-unused-but-set-variable \
+ -Wno-unused-variable
+}
+
+src_compile() {
+ emake \
+ CC="$(tc-getCC)" \
+ CPP="$(tc-getCXX)" \
+ CFLAGS="" \
+ CXXFLAGS="" \
+ EXTRA_FLAGS="${LDFLAGS}" \
+ RELEASE_FLAGS="${CXXFLAGS}" \
+ WITH_TBB="$(usex tbb 1 0)"
+}
+
+src_install() {
+ dobin ${PN} ${PN}-*
+
+ exeinto /usr/libexec/${PN}
+ doexe scripts/*
+
+ newman MANUAL ${PN}.1
+ einstalldocs
+
+ if use examples; then
+ insinto /usr/share/${PN}
+ doins -r genomes indexes
+ fi
+}
diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch
b/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch
new file mode 100644
index 000..78b9c01
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch
@@ -0,0 +1,17 @@
+Description: Change class name of _Context_LSS
+ New version 1.4 of SeQan uses a different name of the class.
+Forwarded: no
+Author: Gert Wollny
+Last-Update: 2014-100-06
+
+--- a/diff_sample.h
b/diff_sample.h
+@@ -856,7 +856,7 @@ void DifferenceCoverSample::build(
+ {
+ Timer timer(cout, " Invoking Larsson-Sadakane on ranks time:
", this->verbose());
+ VMSG_NL(" Invoking Larsson-Sadakane on ranks");
+- _Context_LSS c;
++ ContextLss_ c;
+ c.suffixsort(
+ (TIndexOff*)begin(_isaPrime, Standard()),
+ (TIndexOff*)begin(sPrime, Standard()),
diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch
b/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch
new file mode 100644
index 000..af7f7f6
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch
@@ -0,0 +1,42 @@
+Description: Proper type-casting in using seqan::_setBegin().
+ Required by newer versions of GCC.
+Forwarded: no
+Author: Ognyan Kulev
+Last-Update: 2013-04-18
+
+--- a/pat.h
b/pat.h
+@@ -82,20 +82,20 @@ struct ReadBuf {
+ ~ReadBuf() {
+ clearAll(); reset();
+ // Prevent seqan from trying to free buffers
+- _setBegin(patFw, NULL);
+- _setBegin(patRc, NULL);
+- _setBegin(qual, NULL);
+- _setBegin(patFwRev, NULL);
+- _setBegin(patRcRev, NULL);
+-
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/
commit: 369678cffc9f7ecae414f3800f01a2c2251e8669
Author: Justin Lecher gentoo org>
AuthorDate: Sat Dec 26 18:02:47 2015 +
Commit: Justin Lecher gentoo org>
CommitDate: Sat Dec 26 18:02:47 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=369678cf
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 gentoo.org>
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 deletions(-)
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index c692c89..1291400 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 c26c986..000
--- 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 3c8a1e1..000
--- 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
-+static inline void reverseInPlace(TStr& s) {
-+ typedef typename Value::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
--static inline void reverseInPlace(TStr& s) {
-- typedef typename Value::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.
- */
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
commit: f2f3752753b3b078ecf3c8e3b38859e932b7784c
Author: Justin Lecher gentoo org>
AuthorDate: Sat Dec 26 18:05:43 2015 +
Commit: Justin Lecher gentoo org>
CommitDate: Sat Dec 26 18:05:43 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f2f37527
sci-biology/bowtie: Chop DESCRIPTION to 80 chars
Package-Manager: portage-2.2.26
Signed-off-by: Justin Lecher gentoo.org>
sci-biology/bowtie/bowtie-2.2.6.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/bowtie/bowtie-2.2.6.ebuild
b/sci-biology/bowtie/bowtie-2.2.6.ebuild
index 36b1aa5..eb29c05 100644
--- a/sci-biology/bowtie/bowtie-2.2.6.ebuild
+++ b/sci-biology/bowtie/bowtie-2.2.6.ebuild
@@ -6,7 +6,7 @@ EAPI=5
inherit eutils toolchain-funcs
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data,
allowing for gaps"
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/";
SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
commit: e143c824a96f9dc58f875e769edc5197f8d4fb65
Author: Agostino Sarubbo gentoo org>
AuthorDate: Fri Dec 25 16:20:04 2015 +
Commit: Agostino Sarubbo gentoo org>
CommitDate: Fri Dec 25 16:20:04 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e143c824
sci-biology/bowtie: x86 stable wrt bug #569706
Package-Manager: portage-2.2.24
RepoMan-Options: --include-arches="x86"
Signed-off-by: Agostino Sarubbo gentoo.org>
sci-biology/bowtie/bowtie-1.1.2.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/bowtie/bowtie-1.1.2.ebuild
b/sci-biology/bowtie/bowtie-1.1.2.ebuild
index c39d7d4..f879653 100644
--- a/sci-biology/bowtie/bowtie-1.1.2.ebuild
+++ b/sci-biology/bowtie/bowtie-1.1.2.ebuild
@@ -12,7 +12,7 @@ SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
LICENSE="Artistic"
SLOT="1"
-KEYWORDS="amd64 ~x86 ~x64-macos"
+KEYWORDS="amd64 x86 ~x64-macos"
IUSE="examples +tbb"
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
commit: 61b5a70cfc5a969ba20675c55b70ee02a7c6e854
Author: Agostino Sarubbo gentoo org>
AuthorDate: Fri Dec 25 15:41:56 2015 +
Commit: Agostino Sarubbo gentoo org>
CommitDate: Fri Dec 25 15:41:56 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=61b5a70c
sci-biology/bowtie: amd64 stable wrt bug #569708
Package-Manager: portage-2.2.24
RepoMan-Options: --include-arches="amd64"
Signed-off-by: Agostino Sarubbo gentoo.org>
sci-biology/bowtie/bowtie-2.2.6.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/bowtie/bowtie-2.2.6.ebuild
b/sci-biology/bowtie/bowtie-2.2.6.ebuild
index 8906450..9e24040 100644
--- a/sci-biology/bowtie/bowtie-2.2.6.ebuild
+++ b/sci-biology/bowtie/bowtie-2.2.6.ebuild
@@ -12,7 +12,7 @@
SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source
LICENSE="GPL-3"
SLOT="2"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="amd64 ~x86"
IUSE="examples cpu_flags_x86_sse2 +tbb"
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
commit: 62f64bf8cd5d10ea03ec75418e188334aa97ffd5
Author: Agostino Sarubbo gentoo org>
AuthorDate: Fri Dec 25 15:42:02 2015 +
Commit: Agostino Sarubbo gentoo org>
CommitDate: Fri Dec 25 15:42:02 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=62f64bf8
sci-biology/bowtie: amd64 stable wrt bug #569706
Package-Manager: portage-2.2.24
RepoMan-Options: --include-arches="amd64"
Signed-off-by: Agostino Sarubbo gentoo.org>
sci-biology/bowtie/bowtie-1.1.2.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/bowtie/bowtie-1.1.2.ebuild
b/sci-biology/bowtie/bowtie-1.1.2.ebuild
index a4a8b5b..c39d7d4 100644
--- a/sci-biology/bowtie/bowtie-1.1.2.ebuild
+++ b/sci-biology/bowtie/bowtie-1.1.2.ebuild
@@ -12,7 +12,7 @@ SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
LICENSE="Artistic"
SLOT="1"
-KEYWORDS="~amd64 ~x86 ~x64-macos"
+KEYWORDS="amd64 ~x86 ~x64-macos"
IUSE="examples +tbb"
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
commit: 5660b0815cc329a4983ec40012e883aafe11acee Author: Ted Tanberry gmail com> AuthorDate: Sun Oct 11 07:51:55 2015 + Commit: Justin Lecher gentoo org> CommitDate: Wed Oct 14 12:47:58 2015 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5660b081 sci-biology/bowtie-1.1.2: Enable 'tbb' USE flag by default sci-biology/bowtie/bowtie-1.1.2.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/bowtie/bowtie-1.1.2.ebuild b/sci-biology/bowtie/bowtie-1.1.2.ebuild index 882d1a1..a4a8b5b 100644 --- a/sci-biology/bowtie/bowtie-1.1.2.ebuild +++ b/sci-biology/bowtie/bowtie-1.1.2.ebuild @@ -14,7 +14,7 @@ LICENSE="Artistic" SLOT="1" KEYWORDS="~amd64 ~x86 ~x64-macos" -IUSE="examples tbb" +IUSE="examples +tbb" DEPEND="app-arch/unzip tbb? ( dev-cpp/tbb )"
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/
commit: ddbfba3594bda0b32f359e057555d477ffbced1e
Author: Ted Tanberry gmail com>
AuthorDate: Sat Oct 10 19:04:45 2015 +
Commit: Justin Lecher gentoo org>
CommitDate: Wed Oct 14 12:47:58 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ddbfba35
sci-biology/bowtie: version bump, SLOT major version
sci-biology/bowtie is now SLOTed, in order to allow for a
parallel installation with bowtie2. In addition, the latest
bowtie now supports dev-cpp/tbb with 'tbb' USE flag.
sci-biology/bowtie/Manifest| 4 +-
sci-biology/bowtie/bowtie-0.12.8.ebuild| 44
sci-biology/bowtie/bowtie-1.0.0.ebuild | 42
sci-biology/bowtie/bowtie-1.1.2.ebuild | 58 ++
.../bowtie/files/bowtie-0.12.8-gcc-47.patch| 45 -
.../bowtie-1.1.2-tbb-tinythread-missing.patch | 14 ++
sci-biology/bowtie/metadata.xml| 5 ++
7 files changed, 79 insertions(+), 133 deletions(-)
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index 1345a9e..1291400 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,2 +1,2 @@
-DIST bowtie-0.12.8-src.zip 15569919 SHA256
f074a0f25e156976c4951fd69651d60caab925af9829054d107ec8b19af3082d SHA512
824eddd7db24177f7e15b90fb93a0426c2b8cee4dbcac2707f4cc7e7e42bafcad3775382b79d9b4d679e0c4b5c17a1b79ad134e91a968037336b34c6262e9c48
WHIRLPOOL
7056444822e7a0de619dcab933a7870ebe7db52008f3dbb2dd72aa189325d7ca4c353133d77150ec67c414e005a834458538f57746b13fd20f06bc7289869800
-DIST bowtie-1.0.0-src.zip 7710572 SHA256
51e434a78e053301f82ae56f4e94f71f97b19f7175324777a7305c8f88c5bac5 SHA512
d867a61c9d4caa2fbe8161b93acc9ccf04294055796a82ccf8d6456019e97299d90d9f16492f873606ae394bbc735108fc97ddf4e5d576a7376f3f9744118831
WHIRLPOOL
a70d6516db8ee0c8838795e3b1df0ae1986342cee5dcafd80a39b06cb07ece79d7ebfc6e88b36625d9b33f4f42f559364f42dd4d881fd729c27eac9e673951a1
+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 c26c986..000
--- 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/bowtie-1.0.0.ebuild
b/sci-biology/bowtie/bowtie-1.0.0.ebuild
deleted file mode 100644
index b818119..000
--- a/sci-biology/bowtie/bowtie-1.0.0.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="An ultrafast memory-efficient short read aligner"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/";
-SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-DEPEND="app-arch/unzip"
-RDEPEND=""
-
-src_compile() {
- unset CFLAGS
- emake \
- CC="$(tc-getCC)" \
- CPP="$(tc-getCXX)" \
- CXX="$(tc-getCXX)" \
- EXTRA_FLAGS="${LDFLAGS}" \
-
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
commit: 50fe91c03b9c8431a871463ee75ae68bdfc8a171
Author: Ted Tanberry gmail com>
AuthorDate: Sun Oct 11 08:04:43 2015 +
Commit: Justin Lecher gentoo org>
CommitDate: Wed Oct 14 12:47:58 2015 +
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 000..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 000..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
++static inline void reverseInPlace(TStr& s) {
++ typedef typename Value::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
+-static inline void reverseInPlace(TStr& s) {
+- typedef typename Value::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.
+ */
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
commit: a5cdb5129aa0e80c0f8883863db3b6a9bf00d0fd
Author: Ted Tanberry gmail com>
AuthorDate: Sun Oct 11 07:52:57 2015 +
Commit: Justin Lecher gentoo org>
CommitDate: Wed Oct 14 12:47:58 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a5cdb512
sci-biology/bowtie-2.2.6: Enable 'tbb' USE flag by default
sci-biology/bowtie/bowtie-2.2.6.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/bowtie/bowtie-2.2.6.ebuild
b/sci-biology/bowtie/bowtie-2.2.6.ebuild
index c15de56..3cc3837 100644
--- a/sci-biology/bowtie/bowtie-2.2.6.ebuild
+++ b/sci-biology/bowtie/bowtie-2.2.6.ebuild
@@ -14,7 +14,7 @@ LICENSE="GPL-3"
SLOT="2"
KEYWORDS="~amd64 ~x86"
-IUSE="examples cpu_flags_x86_sse2 tbb"
+IUSE="examples cpu_flags_x86_sse2 +tbb"
RDEPEND="dev-lang/perl"
DEPEND="${RDEPEND}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
commit: 92c7d34329f99fec50cecea8d62647653504ab2f
Author: Justin Lecher gentoo org>
AuthorDate: Wed Oct 14 12:45:36 2015 +
Commit: Justin Lecher gentoo org>
CommitDate: Wed Oct 14 12:47:58 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=92c7d343
sci-biology/bowtie: Respect CXX
Package-Manager: portage-2.2.23
Signed-off-by: Justin Lecher gentoo.org>
sci-biology/bowtie/bowtie-2.2.6.ebuild | 1 +
sci-biology/bowtie/metadata.xml| 2 +-
2 files changed, 2 insertions(+), 1 deletion(-)
diff --git a/sci-biology/bowtie/bowtie-2.2.6.ebuild
b/sci-biology/bowtie/bowtie-2.2.6.ebuild
index 3cc3837..8906450 100644
--- a/sci-biology/bowtie/bowtie-2.2.6.ebuild
+++ b/sci-biology/bowtie/bowtie-2.2.6.ebuild
@@ -37,6 +37,7 @@ src_compile() {
emake \
CC="$(tc-getCC)" \
CPP="$(tc-getCXX)" \
+ CXX="$(tc-getCXX)" \
CFLAGS="" \
CXXFLAGS="" \
EXTRA_FLAGS="${LDFLAGS}" \
diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml
index 58f2d36..6e56af7 100644
--- a/sci-biology/bowtie/metadata.xml
+++ b/sci-biology/bowtie/metadata.xml
@@ -6,7 +6,7 @@
bowtie-bio
-Enables building bowtie with the Intel
+Enables building bowtie with the Intel
Threading Building Blocks from dev-cpp/tbb. This
flag is recommended.
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
commit: 1f3b594dde68ff07ecf429b10b2501660adc0f1d
Author: Ted Tanberry gmail com>
AuthorDate: Sat Oct 10 20:18:12 2015 +
Commit: Justin Lecher gentoo org>
CommitDate: Wed Oct 14 12:47:58 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1f3b594d
sci-biology/bowtie: remove REQUIRED_USE
When SSE2 support is not explicitly enabled, the user is
informed by erroring out instead of portage recommending
enabling cpu flags.
sci-biology/bowtie/bowtie-2.2.6.ebuild | 8 +++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/sci-biology/bowtie/bowtie-2.2.6.ebuild
b/sci-biology/bowtie/bowtie-2.2.6.ebuild
index 50aca7e..c15de56 100644
--- a/sci-biology/bowtie/bowtie-2.2.6.ebuild
+++ b/sci-biology/bowtie/bowtie-2.2.6.ebuild
@@ -15,7 +15,6 @@ SLOT="2"
KEYWORDS="~amd64 ~x86"
IUSE="examples cpu_flags_x86_sse2 tbb"
-REQUIRED_USE="cpu_flags_x86_sse2"
RDEPEND="dev-lang/perl"
DEPEND="${RDEPEND}
@@ -27,6 +26,13 @@ S="${WORKDIR}/${PN}2-${PV}"
DOCS=( AUTHORS NEWS TUTORIAL )
HTML_DOCS=( doc/{manual.html,style.css} )
+pkg_pretend() {
+ if ! use cpu_flags_x86_sse2 ; then
+ eerror "This package requires a CPU supporting the SSE2
instruction set."
+ die "SSE2 support missing"
+ fi
+}
+
src_compile() {
emake \
CC="$(tc-getCC)" \
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
commit: 5ca4d1505a37f273d7eaee41f89b676381e6305e
Author: Ted Tanberry gmail com>
AuthorDate: Sat Oct 10 19:07:16 2015 +
Commit: Justin Lecher gentoo org>
CommitDate: Wed Oct 14 12:47:58 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5ca4d150
sci-biology/bowtie: Add bowtie2 in SLOT=2
sci-biology/bowtie/bowtie-2.2.6.ebuild | 54 ++
1 file changed, 54 insertions(+)
diff --git a/sci-biology/bowtie/bowtie-2.2.6.ebuild
b/sci-biology/bowtie/bowtie-2.2.6.ebuild
new file mode 100644
index 000..50aca7e
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-2.2.6.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data,
allowing for gaps"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/";
+SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
+
+LICENSE="GPL-3"
+SLOT="2"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="examples cpu_flags_x86_sse2 tbb"
+REQUIRED_USE="cpu_flags_x86_sse2"
+
+RDEPEND="dev-lang/perl"
+DEPEND="${RDEPEND}
+ app-arch/unzip
+ tbb? ( dev-cpp/tbb )"
+
+S="${WORKDIR}/${PN}2-${PV}"
+
+DOCS=( AUTHORS NEWS TUTORIAL )
+HTML_DOCS=( doc/{manual.html,style.css} )
+
+src_compile() {
+ emake \
+ CC="$(tc-getCC)" \
+ CPP="$(tc-getCXX)" \
+ CFLAGS="" \
+ CXXFLAGS="" \
+ EXTRA_FLAGS="${LDFLAGS}" \
+ RELEASE_FLAGS="${CXXFLAGS} -msse2" \
+ WITH_TBB="$(usex tbb 1 0)"
+}
+
+src_install() {
+ dobin ${PN}2 ${PN}2-*
+
+ exeinto /usr/libexec/${PN}2
+ doexe scripts/*
+
+ newman MANUAL ${PN}2.1
+ einstalldocs
+
+ if use examples; then
+ insinto /usr/share/${PN}2
+ doins -r example
+ fi
+}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
commit: 3e53a5793eaa33b60d58c8df34dbf5b6d33b4a6e
Author: Ted Tanberry gmail com>
AuthorDate: Sat Oct 10 19:45:34 2015 +
Commit: Justin Lecher gentoo org>
CommitDate: Wed Oct 14 12:47:58 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3e53a579
sci-biology/bowtie: do not remove -Wall from CXXFLAGS
Retain -Wall in CXXFLAGS in bowtie-1.1.2
sci-biology/bowtie/bowtie-1.1.2.ebuild | 3 ---
1 file changed, 3 deletions(-)
diff --git a/sci-biology/bowtie/bowtie-1.1.2.ebuild
b/sci-biology/bowtie/bowtie-1.1.2.ebuild
index 55eec50..882d1a1 100644
--- a/sci-biology/bowtie/bowtie-1.1.2.ebuild
+++ b/sci-biology/bowtie/bowtie-1.1.2.ebuild
@@ -24,9 +24,6 @@ DOCS=( AUTHORS NEWS TUTORIAL doc/README )
HTML_DOCS=( doc/{manual.html,style.css} )
src_prepare() {
- # Suppress useless -Wall pollution
- sed -i 's/\-Wall/\-Wno-enum-compare/g' Makefile || die
-
# always include tinythread.cpp
epatch "${FILESDIR}/${P}-tbb-tinythread-missing.patch"
}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/files/
commit: 40d195052459047265fc6d4a37330fae2151120a Author: Ted Tanberry gmail com> AuthorDate: Sat Oct 10 19:56:10 2015 + Commit: Justin Lecher gentoo org> CommitDate: Wed Oct 14 12:47:58 2015 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=40d19505 sci-biology/bowtie: include descriptive header in patch sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch | 4 1 file changed, 4 insertions(+) diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch b/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch index 2a081ff..bc0f1d0 100644 --- a/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch +++ b/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch @@ -1,3 +1,7 @@ +Fixes missing tinythread.cpp when using TBB: + +ebwt_search.cpp:(.text+0x91bb): undefined reference to `tthread::thread::join()' + --- bowtie-1.1.2/Makefile +++ bowtie-1.1.2/Makefile @@ -106,10 +106,7 @@
