* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
@ 2015-10-14 12:48 Justin Lecher
0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2015-10-14 12:48 UTC (permalink / raw
To: gentoo-commits
commit: 92c7d34329f99fec50cecea8d62647653504ab2f
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Oct 14 12:45:36 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=92c7d343
sci-biology/bowtie: Respect CXX
Package-Manager: portage-2.2.23
Signed-off-by: Justin Lecher <jlec <AT> 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 @@
<remote-id type="sourceforge">bowtie-bio</remote-id>
</upstream>
<use>
- <flag name='tbb'>Enables building bowtie with the Intel
+ <flag name="tbb">Enables building bowtie with the Intel
Threading Building Blocks from <pkg>dev-cpp/tbb</pkg>. This
flag is recommended.</flag>
</use>
^ permalink raw reply related [flat|nested] 17+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
@ 2015-10-14 12:48 Justin Lecher
0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2015-10-14 12:48 UTC (permalink / raw
To: gentoo-commits
commit: 5660b0815cc329a4983ec40012e883aafe11acee
Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Sun Oct 11 07:51:55 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=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 )"
^ permalink raw reply related [flat|nested] 17+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
@ 2015-10-14 12:48 Justin Lecher
0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2015-10-14 12:48 UTC (permalink / raw
To: gentoo-commits
commit: 1f3b594dde68ff07ecf429b10b2501660adc0f1d
Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Sat Oct 10 20:18:12 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=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="$(tc-getCC)" \
^ permalink raw reply related [flat|nested] 17+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
@ 2015-10-14 12:48 Justin Lecher
0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2015-10-14 12:48 UTC (permalink / raw
To: gentoo-commits
commit: 3e53a5793eaa33b60d58c8df34dbf5b6d33b4a6e
Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Sat Oct 10 19:45:34 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Oct 14 12:47:58 2015 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3e53a579
sci-biology/bowtie: do not remove -Wall from CXXFLAGS
Retain -Wall in CXXFLAGS in bowtie-1.1.2
sci-biology/bowtie/bowtie-1.1.2.ebuild | 3 ---
1 file changed, 3 deletions(-)
diff --git a/sci-biology/bowtie/bowtie-1.1.2.ebuild b/sci-biology/bowtie/bowtie-1.1.2.ebuild
index 55eec50..882d1a1 100644
--- a/sci-biology/bowtie/bowtie-1.1.2.ebuild
+++ b/sci-biology/bowtie/bowtie-1.1.2.ebuild
@@ -24,9 +24,6 @@ DOCS=( AUTHORS NEWS TUTORIAL doc/README )
HTML_DOCS=( doc/{manual.html,style.css} )
src_prepare() {
- # Suppress useless -Wall pollution
- sed -i 's/\-Wall/\-Wno-enum-compare/g' Makefile || die
-
# always include tinythread.cpp
epatch "${FILESDIR}/${P}-tbb-tinythread-missing.patch"
}
^ permalink raw reply related [flat|nested] 17+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
@ 2015-10-14 12:48 Justin Lecher
0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2015-10-14 12:48 UTC (permalink / raw
To: gentoo-commits
commit: a5cdb5129aa0e80c0f8883863db3b6a9bf00d0fd
Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Sun Oct 11 07:52:57 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Oct 14 12:47:58 2015 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a5cdb512
sci-biology/bowtie-2.2.6: Enable 'tbb' USE flag by default
sci-biology/bowtie/bowtie-2.2.6.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/bowtie/bowtie-2.2.6.ebuild b/sci-biology/bowtie/bowtie-2.2.6.ebuild
index c15de56..3cc3837 100644
--- a/sci-biology/bowtie/bowtie-2.2.6.ebuild
+++ b/sci-biology/bowtie/bowtie-2.2.6.ebuild
@@ -14,7 +14,7 @@ LICENSE="GPL-3"
SLOT="2"
KEYWORDS="~amd64 ~x86"
-IUSE="examples cpu_flags_x86_sse2 tbb"
+IUSE="examples cpu_flags_x86_sse2 +tbb"
RDEPEND="dev-lang/perl"
DEPEND="${RDEPEND}
^ permalink raw reply related [flat|nested] 17+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
@ 2015-10-14 12:48 Justin Lecher
0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2015-10-14 12:48 UTC (permalink / raw
To: gentoo-commits
commit: 5ca4d1505a37f273d7eaee41f89b676381e6305e
Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Sat Oct 10 19:07:16 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=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 0000000..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
+}
^ permalink raw reply related [flat|nested] 17+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
@ 2015-12-25 15:42 Agostino Sarubbo
0 siblings, 0 replies; 17+ messages in thread
From: Agostino Sarubbo @ 2015-12-25 15:42 UTC (permalink / raw
To: gentoo-commits
commit: 62f64bf8cd5d10ea03ec75418e188334aa97ffd5
Author: Agostino Sarubbo <ago <AT> gentoo <DOT> org>
AuthorDate: Fri Dec 25 15:42:02 2015 +0000
Commit: Agostino Sarubbo <ago <AT> gentoo <DOT> org>
CommitDate: Fri Dec 25 15:42:02 2015 +0000
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 <ago <AT> 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/${P}-src.zip"
LICENSE="Artistic"
SLOT="1"
-KEYWORDS="~amd64 ~x86 ~x64-macos"
+KEYWORDS="amd64 ~x86 ~x64-macos"
IUSE="examples +tbb"
^ permalink raw reply related [flat|nested] 17+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
@ 2015-12-25 15:42 Agostino Sarubbo
0 siblings, 0 replies; 17+ messages in thread
From: Agostino Sarubbo @ 2015-12-25 15:42 UTC (permalink / raw
To: gentoo-commits
commit: 61b5a70cfc5a969ba20675c55b70ee02a7c6e854
Author: Agostino Sarubbo <ago <AT> gentoo <DOT> org>
AuthorDate: Fri Dec 25 15:41:56 2015 +0000
Commit: Agostino Sarubbo <ago <AT> gentoo <DOT> org>
CommitDate: Fri Dec 25 15:41:56 2015 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=61b5a70c
sci-biology/bowtie: amd64 stable wrt bug #569708
Package-Manager: portage-2.2.24
RepoMan-Options: --include-arches="amd64"
Signed-off-by: Agostino Sarubbo <ago <AT> gentoo.org>
sci-biology/bowtie/bowtie-2.2.6.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/bowtie/bowtie-2.2.6.ebuild b/sci-biology/bowtie/bowtie-2.2.6.ebuild
index 8906450..9e24040 100644
--- a/sci-biology/bowtie/bowtie-2.2.6.ebuild
+++ b/sci-biology/bowtie/bowtie-2.2.6.ebuild
@@ -12,7 +12,7 @@ SRC_URI="mirror://sourceforge/project/${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"
^ permalink raw reply related [flat|nested] 17+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
@ 2015-12-25 16:20 Agostino Sarubbo
0 siblings, 0 replies; 17+ messages in thread
From: Agostino Sarubbo @ 2015-12-25 16:20 UTC (permalink / raw
To: gentoo-commits
commit: e143c824a96f9dc58f875e769edc5197f8d4fb65
Author: Agostino Sarubbo <ago <AT> gentoo <DOT> org>
AuthorDate: Fri Dec 25 16:20:04 2015 +0000
Commit: Agostino Sarubbo <ago <AT> gentoo <DOT> org>
CommitDate: Fri Dec 25 16:20:04 2015 +0000
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 <ago <AT> 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/${P}-src.zip"
LICENSE="Artistic"
SLOT="1"
-KEYWORDS="amd64 ~x86 ~x64-macos"
+KEYWORDS="amd64 x86 ~x64-macos"
IUSE="examples +tbb"
^ permalink raw reply related [flat|nested] 17+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
@ 2015-12-26 18:05 Justin Lecher
0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2015-12-26 18:05 UTC (permalink / raw
To: gentoo-commits
commit: f2f3752753b3b078ecf3c8e3b38859e932b7784c
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Dec 26 18:05:43 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Dec 26 18:05:43 2015 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f2f37527
sci-biology/bowtie: Chop DESCRIPTION to 80 chars
Package-Manager: portage-2.2.26
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/bowtie/bowtie-2.2.6.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/bowtie/bowtie-2.2.6.ebuild b/sci-biology/bowtie/bowtie-2.2.6.ebuild
index 36b1aa5..eb29c05 100644
--- a/sci-biology/bowtie/bowtie-2.2.6.ebuild
+++ b/sci-biology/bowtie/bowtie-2.2.6.ebuild
@@ -6,7 +6,7 @@ EAPI=5
inherit eutils toolchain-funcs
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data, allowing for gaps"
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"
SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
^ permalink raw reply related [flat|nested] 17+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
@ 2016-04-10 9:48 David Seifert
0 siblings, 0 replies; 17+ messages in thread
From: David Seifert @ 2016-04-10 9:48 UTC (permalink / raw
To: gentoo-commits
commit: c9b8497a77f3a72c025ca02d8fd8bdb024e34189
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Apr 10 09:47:56 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Apr 10 09:48:08 2016 +0000
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 0000000..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
+}
^ permalink raw reply related [flat|nested] 17+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
@ 2016-06-04 21:17 David Seifert
0 siblings, 0 replies; 17+ messages in thread
From: David Seifert @ 2016-06-04 21:17 UTC (permalink / raw
To: gentoo-commits
commit: adf47f7e0b7623ad7740c8226b95a69f978072ba
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 4 21:17:19 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Jun 4 21:17:33 2016 +0000
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 ed8894096997ddd724c8999971a82b14bfa8149a23c040463c6f347ddce070a8c44baeb21bc1adc41a756e0e02c8f4861b967477c2f3469a71ca58b7d3e60aac
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
^ permalink raw reply related [flat|nested] 17+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
@ 2017-12-25 16:09 David Seifert
0 siblings, 0 replies; 17+ messages in thread
From: David Seifert @ 2017-12-25 16:09 UTC (permalink / raw
To: gentoo-commits
commit: 6d8d74d327137358ffb5e4dad142b9c8b280f71c
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Dec 25 09:57:08 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Dec 25 16:08:50 2017 +0000
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..00000000000
--- 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..00000000000
--- 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 ${PN}2.1
- einstalldocs
-
- if use examples; then
- insinto /usr/share/${PN}2
- doins -r example
- fi
-}
^ permalink raw reply related [flat|nested] 17+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
@ 2021-08-01 16:41 David Seifert
0 siblings, 0 replies; 17+ messages in thread
From: David Seifert @ 2021-08-01 16:41 UTC (permalink / raw
To: gentoo-commits
commit: 20633430c439732edc1dd09d5b76acefcaa54c9d
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Aug 1 16:40:40 2021 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Aug 1 16:40:40 2021 +0000
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 <soap <AT> 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 00000000000..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
+}
^ permalink raw reply related [flat|nested] 17+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
@ 2021-08-01 17:02 David Seifert
0 siblings, 0 replies; 17+ messages in thread
From: David Seifert @ 2021-08-01 17:02 UTC (permalink / raw
To: gentoo-commits
commit: e99b33b0d98ad381a2a4ceaab86f86dd5e2d2d00
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Aug 1 17:02:01 2021 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Aug 1 17:02:01 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e99b33b0
sci-biology/bowtie: fix QA issues
Signed-off-by: David Seifert <soap <AT> 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 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">bowtie-bio</remote-id>
- </upstream>
- <use>
- <flag name="tbb">Enables building bowtie with the Intel
- Threading Building Blocks from <pkg>dev-cpp/tbb</pkg>. This
- flag is recommended.</flag>
- </use>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="sourceforge">bowtie-bio</remote-id>
+ </upstream>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 17+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
@ 2023-02-24 7:30 Andrew Ammerlaan
0 siblings, 0 replies; 17+ messages in thread
From: Andrew Ammerlaan @ 2023-02-24 7:30 UTC (permalink / raw
To: gentoo-commits
commit: ad0f0da9f1b0df76d06b2bd4c52ce233ce4c8001
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 24 07:29:55 2023 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Feb 24 07:29:55 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ad0f0da9
sci-biology/bowtie: add 2.5.1
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> 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 000000000000..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
+}
^ permalink raw reply related [flat|nested] 17+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/
@ 2024-07-30 21:13 Pacho Ramos
0 siblings, 0 replies; 17+ messages in thread
From: Pacho Ramos @ 2024-07-30 21:13 UTC (permalink / raw
To: gentoo-commits
commit: 9de8c676fe59c8570f2982846b440973beb8cafd
Author: Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Tue Jul 30 19:40:05 2024 +0000
Commit: Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Tue Jul 30 21:11:51 2024 +0000
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 <pacho <AT> 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
^ permalink raw reply related [flat|nested] 17+ messages in thread
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2015-12-26 18:05 [gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/ Justin Lecher
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2024-07-30 21:13 Pacho Ramos
2023-02-24 7:30 Andrew Ammerlaan
2021-08-01 17:02 David Seifert
2021-08-01 16:41 David Seifert
2017-12-25 16:09 David Seifert
2016-06-04 21:17 David Seifert
2016-04-10 9:48 David Seifert
2015-12-25 16:20 Agostino Sarubbo
2015-12-25 15:42 Agostino Sarubbo
2015-12-25 15:42 Agostino Sarubbo
2015-10-14 12:48 Justin Lecher
2015-10-14 12:48 Justin Lecher
2015-10-14 12:48 Justin Lecher
2015-10-14 12:48 Justin Lecher
2015-10-14 12:48 Justin Lecher
2015-10-14 12:48 Justin Lecher
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