* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
@ 2020-12-30 22:52 Martin Mokrejs
0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2020-12-30 22:52 UTC (permalink / raw
To: gentoo-commits
commit: 7653e736bbdbd6d7373e8015b0b79e1855032f83
Author: Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Wed Dec 30 22:52:06 2020 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Dec 30 22:52:26 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7653e736
sci-biology/bowtie: version bump
the sci-biology/sra_sdk is not complete in Gentoo so bowtie cannot
use this optional dependency (yet)
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>
sci-biology/bowtie/{bowtie-2.4.1.ebuild => bowtie-2.4.2.ebuild} | 9 ++++++++-
1 file changed, 8 insertions(+), 1 deletion(-)
diff --git a/sci-biology/bowtie/bowtie-2.4.1.ebuild b/sci-biology/bowtie/bowtie-2.4.2.ebuild
similarity index 86%
rename from sci-biology/bowtie/bowtie-2.4.1.ebuild
rename to sci-biology/bowtie/bowtie-2.4.2.ebuild
index a4d6837ba..3cd8c2cdc 100644
--- a/sci-biology/bowtie/bowtie-2.4.1.ebuild
+++ b/sci-biology/bowtie/bowtie-2.4.2.ebuild
@@ -14,13 +14,15 @@ LICENSE="GPL-3"
SLOT="2"
KEYWORDS="~amd64 ~x86"
-IUSE="examples cpu_flags_x86_sse2 +tbb"
+IUSE="examples cpu_flags_x86_sse2 +tbb" # sra
+# IUSE=sra Use sra-toolkit to download input datasets on the fly.
RDEPEND="dev-lang/perl
tbb? ( dev-cpp/tbb )"
DEPEND="${RDEPEND}
app-arch/unzip
sys-libs/readline"
+# sra? ( sci-biology/sra_sdk )"
S="${WORKDIR}/${PN}2-${PV}"
@@ -42,6 +44,7 @@ src_compile() {
EXTRA_FLAGS="${LDFLAGS}" \
RELEASE_FLAGS="${CXXFLAGS} -msse2" \
WITH_TBB="$(usex tbb 1 0)"
+ # USE_SRA="$(usex sra 1 0)"
}
src_install() {
@@ -58,3 +61,7 @@ src_install() {
doins -r example
fi
}
+
+src_test(){
+ emake test
+}
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
@ 2021-03-17 10:37 Andrew Ammerlaan
0 siblings, 0 replies; 17+ messages in thread
From: Andrew Ammerlaan @ 2021-03-17 10:37 UTC (permalink / raw
To: gentoo-commits
commit: 77a54a4d9f64ce2bfff0ef2928500cefd5cb1b9d
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Mar 17 10:37:01 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Mar 17 10:37:01 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=77a54a4d
sci-biology/bowtie: add version 1.3.0
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/bowtie/bowtie-1.3.0.ebuild | 63 ++++++++++++++++++++++++++++++++++
1 file changed, 63 insertions(+)
diff --git a/sci-biology/bowtie/bowtie-1.3.0.ebuild b/sci-biology/bowtie/bowtie-1.3.0.ebuild
new file mode 100644
index 000000000..118cc1303
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-1.3.0.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit flag-o-matic toolchain-funcs
+
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/"
+SRC_URI="https://github.com/BenLangmead/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="1"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="examples +tbb"
+
+RDEPEND="tbb? ( dev-cpp/tbb )"
+DEPEND="${RDEPEND}
+ app-arch/unzip"
+# sci-biology/seqan:1.4"
+
+DOCS=( AUTHORS NEWS TUTORIAL doc/README )
+HTML_DOCS=( doc/{manual.html,style.css} )
+
+src_prepare() {
+ default
+
+ # remove bundled library of headers, 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
+}
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
@ 2021-03-16 18:15 Andrew Ammerlaan
0 siblings, 0 replies; 17+ messages in thread
From: Andrew Ammerlaan @ 2021-03-16 18:15 UTC (permalink / raw
To: gentoo-commits
commit: ecf85a996b942336d7f2e23c11e3acd723914e36
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Mar 16 18:15:31 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Mar 16 18:15:31 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ecf85a99
sci-biology/bowtie: EAPI bump bowtie-1
patch does not apply (anymore)
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
index f7a1b92d4..857bc9cd1 100644
--- a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
+++ b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
inherit flag-o-matic toolchain-funcs git-r3
@@ -25,7 +25,7 @@ DEPEND="${RDEPEND}
DOCS=( AUTHORS NEWS TUTORIAL doc/README )
HTML_DOCS=( doc/{manual.html,style.css} )
-PATCHES=( "${FILESDIR}/bowtie-1.2.2-fix-isa-return-type.patch" )
+#PATCHES=( "${FILESDIR}/bowtie-1.2.2-fix-isa-return-type.patch" )
# not needed
# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b
#
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
@ 2021-03-06 10:02 Andrew Ammerlaan
0 siblings, 0 replies; 17+ messages in thread
From: Andrew Ammerlaan @ 2021-03-06 10:02 UTC (permalink / raw
To: gentoo-commits
commit: 3b6fcb10881cdda5486994a4b3e6a6c1476f6946
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar 6 10:02:19 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar 6 10:02:19 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3b6fcb10
sci-biology/bowtie: EAPI bump
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/bowtie/bowtie-2.4.2.ebuild | 9 ++-------
1 file changed, 2 insertions(+), 7 deletions(-)
diff --git a/sci-biology/bowtie/bowtie-2.4.2.ebuild b/sci-biology/bowtie/bowtie-2.4.2.ebuild
index 3cd8c2cdc..03cf3f8a9 100644
--- a/sci-biology/bowtie/bowtie-2.4.2.ebuild
+++ b/sci-biology/bowtie/bowtie-2.4.2.ebuild
@@ -1,13 +1,12 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
inherit toolchain-funcs
DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"
-SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
SRC_URI="https://github.com/BenLangmead/${PN}2/archive/v${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-3"
@@ -61,7 +60,3 @@ src_install() {
doins -r example
fi
}
-
-src_test(){
- emake test
-}
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
@ 2020-02-28 23:07 Martin Mokrejs
0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2020-02-28 23:07 UTC (permalink / raw
To: gentoo-commits
commit: 1f6479da30739c1e62b5df19384df7e5c2674e14
Author: Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Fri Feb 28 23:06:48 2020 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Feb 28 23:07:25 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1f6479da
sci-biology/bowtie: version bump (bugfix release)
Package-Manager: Portage-2.3.87, Repoman-2.3.20
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>
sci-biology/bowtie/{bowtie-2.4.0.ebuild => bowtie-2.4.1.ebuild} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/sci-biology/bowtie/bowtie-2.4.0.ebuild b/sci-biology/bowtie/bowtie-2.4.1.ebuild
similarity index 100%
rename from sci-biology/bowtie/bowtie-2.4.0.ebuild
rename to sci-biology/bowtie/bowtie-2.4.1.ebuild
^ permalink raw reply [flat|nested] 17+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
@ 2020-02-26 8:49 Martin Mokrejs
0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2020-02-26 8:49 UTC (permalink / raw
To: gentoo-commits
commit: 731ea47715109fabdd7cc3944b6c522509619f56
Author: Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Wed Feb 26 08:48:45 2020 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Feb 26 08:49:28 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=731ea477
sci-biology/bowtie: version bump to 2.4.0, drop old 2.3.5
Package-Manager: Portage-2.3.87, Repoman-2.3.20
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>
.../bowtie/bowtie-1.2.2_beta20190219.ebuild | 2 +-
sci-biology/bowtie/bowtie-2.3.5-r1.ebuild | 63 ----------------------
.../{bowtie-2.3.5.1.ebuild => bowtie-2.4.0.ebuild} | 2 +-
3 files changed, 2 insertions(+), 65 deletions(-)
diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
index fcf0b4516..f7a1b92d4 100644
--- a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
+++ b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
diff --git a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
deleted file mode 100644
index 2a6fc04eb..000000000
--- a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# 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"
-SRC_URI="https://github.com/BenLangmead/${PN}2/releases/download/v${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="${RDEPEND}
- app-arch/unzip
- sys-libs/readline"
-
-S="${WORKDIR}/${PN}2-${PV}"
-
-DOCS=( AUTHORS NEWS TUTORIAL )
-HTML_DOCS=( doc/{manual.html,style.css} )
-#PATCHES=( "${FILESDIR}/${P}-fix-c++14.patch" ) # needs 2.3.4.3 update
-PATCHES=( "${FILESDIR}"/bowtie-2.3.5-fix-interleaved.patch
- "${FILESDIR}"/bowtie-2.3.5-fix-fifo.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="$(tc-getCXX)" \
- EXTRA_FLAGS="${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/bowtie-2.3.5.1.ebuild b/sci-biology/bowtie/bowtie-2.4.0.ebuild
similarity index 97%
rename from sci-biology/bowtie/bowtie-2.3.5.1.ebuild
rename to sci-biology/bowtie/bowtie-2.4.0.ebuild
index c2fef8667..a4d6837ba 100644
--- a/sci-biology/bowtie/bowtie-2.3.5.1.ebuild
+++ b/sci-biology/bowtie/bowtie-2.4.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
@ 2019-03-25 11:21 Martin Mokrejs
0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2019-03-25 11:21 UTC (permalink / raw
To: gentoo-commits
commit: 922b05adcf80432d8e8212128b90b456b8ad3fc5
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 25 11:20:55 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 25 11:20:55 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=922b05ad
sci-biology/bowtie: update SRC_URI and hash for 2.3.5
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/bowtie/{bowtie-2.3.4.3.ebuild => bowtie-2.3.5.ebuild} | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-biology/bowtie/bowtie-2.3.4.3.ebuild b/sci-biology/bowtie/bowtie-2.3.5.ebuild
similarity index 93%
rename from sci-biology/bowtie/bowtie-2.3.4.3.ebuild
rename to sci-biology/bowtie/bowtie-2.3.5.ebuild
index eea3059cf..dd4d8be66 100644
--- a/sci-biology/bowtie/bowtie-2.3.4.3.ebuild
+++ b/sci-biology/bowtie/bowtie-2.3.5.ebuild
@@ -8,6 +8,7 @@ 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-${PV}-source.zip"
+SRC_URI="https://github.com/BenLangmead/${PN}2/releases/download/v${PV}/${PN}2-${PV}-source.zip"
LICENSE="GPL-3"
SLOT="2"
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
@ 2019-02-19 11:26 Martin Mokrejs
0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2019-02-19 11:26 UTC (permalink / raw
To: gentoo-commits
commit: b6846dd42e04e42c0103983272b6db0db248f75a
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Feb 19 11:26:14 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Feb 19 11:26:14 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b6846dd4
sci-biology/bowtie: removing not working -1.2.2 ebuild
Package-Manager: Portage-2.3.61, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/bowtie/bowtie-1.2.2.ebuild | 77 ----------------------------------
1 file changed, 77 deletions(-)
diff --git a/sci-biology/bowtie/bowtie-1.2.2.ebuild b/sci-biology/bowtie/bowtie-1.2.2.ebuild
deleted file mode 100644
index cae085bff..000000000
--- a/sci-biology/bowtie/bowtie-1.2.2.ebuild
+++ /dev/null
@@ -1,77 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit flag-o-matic toolchain-funcs
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/"
-SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
-
-LICENSE="Artistic"
-SLOT="1"
-KEYWORDS=""
-
-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}/${P}-fix-Intel-compilation.patch"
- "${FILESDIR}/${P}-unbundle-seqan.patch"
-)
-# other patches to be still considered
-# "${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}/${P}-tbb-tinythread-missing.patch"
-#)
-
-src_prepare() {
- default
-
- # remove bundled libraries, use system seqan 1.4
- rm -rf SeqAn-1.1/ third_party/ || die
-
- # innocuous non-security flags, prevent log pollution
- append-cxxflags \
- -Wno-unused-local-typedefs \
- -Wno-unused-but-set-variable \
- -Wno-unused-variable
-}
-
-src_compile() {
- emake \
- CC="$(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
-}
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
@ 2019-02-19 11:24 Martin Mokrejs
0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2019-02-19 11:24 UTC (permalink / raw
To: gentoo-commits
commit: 51f9e3636c1422b40200dcc11c4122f356cfe4de
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Feb 19 11:24:18 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Feb 19 11:24:18 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=51f9e363
sci-biology/bowtie: removing -9999 ebuild
Package-Manager: Portage-2.3.61, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/bowtie/bowtie-9999.ebuild | 81 -----------------------------------
1 file changed, 81 deletions(-)
diff --git a/sci-biology/bowtie/bowtie-9999.ebuild b/sci-biology/bowtie/bowtie-9999.ebuild
deleted file mode 100644
index d54d0a544..000000000
--- a/sci-biology/bowtie/bowtie-9999.ebuild
+++ /dev/null
@@ -1,81 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit flag-o-matic toolchain-funcs git-r3
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/"
-EGIT_REPO_URI="https://github.com/BenLangmead/bowtie.git"
-EGIT_BRANCH="bug_fixes"
-
-LICENSE="Artistic"
-SLOT="1"
-KEYWORDS=""
-
-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}/bowtie-9999-fix-isa-return-type.patch" )
-# not needed
-# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b
-#PATCHES=(
-# "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch"
-# "${FILESDIR}/${P}-fix-Intel-compilation.patch"
-# "${FILESDIR}/${P}-unbundle-seqan.patch"
-#)
-# other patches to be still considered
-# "${FILESDIR}/${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"
-#)
-
-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
-}
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
@ 2015-10-12 6:51 Marius Brehler
0 siblings, 0 replies; 17+ messages in thread
From: Marius Brehler @ 2015-10-12 6:51 UTC (permalink / raw
To: gentoo-commits
commit: 87642b198308aa88ce351b935b79a58a08cf164b
Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Sat Oct 10 17:48:48 2015 +0000
Commit: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Sat Oct 10 17:48:48 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=87642b19
sci-biology/bowtie: Version bump to 2.2.6
dev-cpp/tbb is now supported with 'tbb' USE flag.
sci-biology/bowtie/ChangeLog | 6 ++++
sci-biology/bowtie/bowtie-2.2.6.ebuild | 54 ++++++++++++++++++++++++++++++++++
2 files changed, 60 insertions(+)
diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog
index 42bdbdf..6530be0 100644
--- a/sci-biology/bowtie/ChangeLog
+++ b/sci-biology/bowtie/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+*bowtie-2.2.6 (10 Oct 2015)
+
+ 10 Oct 2015; Ted Tanberry <ted.tanberry@gmail.com> +bowtie-2.2.6.ebuild:
+ sci-biology/bowtie: Version bump to 2.2.6, support dev-cpp/tbb with
+ USE flag.
+
*bowtie-1.1.2 (10 Oct 2015)
10 Oct 2015; Ted Tanberry <ted.tanberry@gmail.com> +bowtie-1.1.2.ebuild,
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..fce2985
--- /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="Short read aligner supporting gaps, matches to N nucleotides, no end-to-end requirement"
+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] proj/sci:master commit in: sci-biology/bowtie/
@ 2015-10-12 6:51 Marius Brehler
0 siblings, 0 replies; 17+ messages in thread
From: Marius Brehler @ 2015-10-12 6:51 UTC (permalink / raw
To: gentoo-commits
commit: 05f13955c6ce57de4194483c2e1e15744d02cf5d
Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Sat Oct 10 17:50:43 2015 +0000
Commit: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Sat Oct 10 17:50:43 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=05f13955
sci-biology/bowtie: Use 'usex' instead of defining TBB variable.
sci-biology/bowtie/bowtie-1.1.2.ebuild | 8 +-------
1 file changed, 1 insertion(+), 7 deletions(-)
diff --git a/sci-biology/bowtie/bowtie-1.1.2.ebuild b/sci-biology/bowtie/bowtie-1.1.2.ebuild
index e443686..1988f6b 100644
--- a/sci-biology/bowtie/bowtie-1.1.2.ebuild
+++ b/sci-biology/bowtie/bowtie-1.1.2.ebuild
@@ -32,12 +32,6 @@ src_prepare() {
}
src_compile() {
- if use tbb ; then
- TBB="1"
- else
- TBB="0"
- fi
-
emake \
CC="$(tc-getCC)" \
CPP="$(tc-getCXX)" \
@@ -45,7 +39,7 @@ src_compile() {
CXXFLAGS="" \
EXTRA_FLAGS="${LDFLAGS}" \
RELEASE_FLAGS="${CXXFLAGS}" \
- WITH_TBB="${TBB}"
+ WITH_TBB="$(usex tbb 1 0)"
}
src_install() {
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
@ 2015-05-01 20:38 Martin Mokrejs
0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2015-05-01 20:38 UTC (permalink / raw
To: gentoo-commits
commit: a6949bfe7f087ab37f5ebf875ecc154dda9d8593
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri May 1 20:37:44 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri May 1 20:37:44 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a6949bfe
sci-biology/bowtie: clarified package descriptions (bowtie1 vs. bowtie2)
Package-Manager: portage-2.2.18
sci-biology/bowtie/ChangeLog | 4 ++++
sci-biology/bowtie/bowtie-1.1.1.ebuild | 2 +-
sci-biology/bowtie/bowtie-2.2.3.ebuild | 2 +-
sci-biology/bowtie/bowtie-2.2.5.ebuild | 2 +-
4 files changed, 7 insertions(+), 3 deletions(-)
diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog
index 0bc0afa..4be1ee3 100644
--- a/sci-biology/bowtie/ChangeLog
+++ b/sci-biology/bowtie/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 01 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bowtie-1.1.1.ebuild,
+ bowtie-2.2.3.ebuild, bowtie-2.2.5.ebuild:
+ sci-biology/bowtie: clarified package descriptions (bowtie1 vs. bowtie2)
+
*bowtie-2.2.3 (27 Apr 2015)
*bowtie-2.2.5 (27 Apr 2015)
diff --git a/sci-biology/bowtie/bowtie-1.1.1.ebuild b/sci-biology/bowtie/bowtie-1.1.1.ebuild
index 536e9d8..e6e5c3a 100644
--- a/sci-biology/bowtie/bowtie-1.1.1.ebuild
+++ b/sci-biology/bowtie/bowtie-1.1.1.ebuild
@@ -6,7 +6,7 @@ EAPI=5
inherit eutils toolchain-funcs
-DESCRIPTION="An ultrafast memory-efficient short read aligner"
+DESCRIPTION="Short read (below 50nt) aligner requiring end-to-end match, no gaps"
HOMEPAGE="http://bowtie-bio.sourceforge.net/"
SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
diff --git a/sci-biology/bowtie/bowtie-2.2.3.ebuild b/sci-biology/bowtie/bowtie-2.2.3.ebuild
index d8059fc..e987cdb 100644
--- a/sci-biology/bowtie/bowtie-2.2.3.ebuild
+++ b/sci-biology/bowtie/bowtie-2.2.3.ebuild
@@ -6,7 +6,7 @@ EAPI=5
inherit eutils toolchain-funcs
-DESCRIPTION="An ultrafast memory-efficient short read aligner"
+DESCRIPTION="Short read aligner supporting gaps, matches to N nucleotides, no end-to-end requirement"
HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"
SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
diff --git a/sci-biology/bowtie/bowtie-2.2.5.ebuild b/sci-biology/bowtie/bowtie-2.2.5.ebuild
index d8059fc..e987cdb 100644
--- a/sci-biology/bowtie/bowtie-2.2.5.ebuild
+++ b/sci-biology/bowtie/bowtie-2.2.5.ebuild
@@ -6,7 +6,7 @@ EAPI=5
inherit eutils toolchain-funcs
-DESCRIPTION="An ultrafast memory-efficient short read aligner"
+DESCRIPTION="Short read aligner supporting gaps, matches to N nucleotides, no end-to-end requirement"
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] proj/sci:master commit in: sci-biology/bowtie/
@ 2015-04-27 11:01 Martin Mokrejs
0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2015-04-27 11:01 UTC (permalink / raw
To: gentoo-commits
commit: 56eef21f8af41d10246dc582ce51ec09cd514c3e
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Apr 27 11:00:54 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Apr 27 11:00:54 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=56eef21f
sci-biology/bowtie: version bump
Package-Manager: portage-2.2.18
sci-biology/bowtie/ChangeLog | 8 +++++++-
sci-biology/bowtie/{bowtie-2.2.4.ebuild => bowtie-2.2.3.ebuild} | 0
sci-biology/bowtie/{bowtie-2.2.4.ebuild => bowtie-2.2.5.ebuild} | 0
3 files changed, 7 insertions(+), 1 deletion(-)
diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog
index f3d98e2..0bc0afa 100644
--- a/sci-biology/bowtie/ChangeLog
+++ b/sci-biology/bowtie/ChangeLog
@@ -2,10 +2,16 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*bowtie-2.2.3 (27 Apr 2015)
+*bowtie-2.2.5 (27 Apr 2015)
+
+ 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +bowtie-2.2.3.ebuild, +bowtie-2.2.5.ebuild, -bowtie-2.2.4.ebuild:
+ sci-biology/bowtie: version bump
+
06 Feb 2015; Ted Tanberry <ted.tanberry@gmail.com> bowtie-1.1.1.ebuild,
bowtie-2.2.4.ebuild: Version bump, updated ebuild, fixed small build
system bugs
28 Sep 2013; Justin Lecher <jlec@gentoo.org> bowtie-2.1.0.ebuild:
Exchange common variables, fix SRC_URI
-
diff --git a/sci-biology/bowtie/bowtie-2.2.4.ebuild b/sci-biology/bowtie/bowtie-2.2.3.ebuild
similarity index 100%
copy from sci-biology/bowtie/bowtie-2.2.4.ebuild
copy to sci-biology/bowtie/bowtie-2.2.3.ebuild
diff --git a/sci-biology/bowtie/bowtie-2.2.4.ebuild b/sci-biology/bowtie/bowtie-2.2.5.ebuild
similarity index 100%
rename from sci-biology/bowtie/bowtie-2.2.4.ebuild
rename to sci-biology/bowtie/bowtie-2.2.5.ebuild
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
@ 2015-02-08 21:07 Christoph Junghans
0 siblings, 0 replies; 17+ messages in thread
From: Christoph Junghans @ 2015-02-08 21:07 UTC (permalink / raw
To: gentoo-commits
commit: d9b4902dd52631d0ff4cbf2d92a1448c722989fd
Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Sat Feb 7 13:03:26 2015 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Feb 7 13:03:26 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d9b4902d
Added die to sed command for bowtie-1.1.1.ebuild
---
sci-biology/bowtie/bowtie-1.1.1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/bowtie/bowtie-1.1.1.ebuild b/sci-biology/bowtie/bowtie-1.1.1.ebuild
index bc6d514..536e9d8 100644
--- a/sci-biology/bowtie/bowtie-1.1.1.ebuild
+++ b/sci-biology/bowtie/bowtie-1.1.1.ebuild
@@ -24,7 +24,7 @@ HTML_DOCS=( doc/{manual.html,style.css} )
src_prepare() {
# Suppress useless -Wall pollution
- sed -i 's/\-Wall/\-Wno-enum-compare/g' Makefile
+ sed -i 's/\-Wall/\-Wno-enum-compare/g' Makefile || die
}
src_compile() {
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
@ 2015-02-08 21:07 Christoph Junghans
0 siblings, 0 replies; 17+ messages in thread
From: Christoph Junghans @ 2015-02-08 21:07 UTC (permalink / raw
To: gentoo-commits
commit: 60ba53b88755c62f589c3787765bd6f39da78eef
Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Fri Feb 6 08:52:03 2015 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Feb 6 20:24:01 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=60ba53b8
Updated bowtie:{1,2} ebuilds to match current ebuild policy.
---
sci-biology/bowtie/bowtie-1.1.1.ebuild | 29 +++++++++++++++++++----------
sci-biology/bowtie/bowtie-2.2.4.ebuild | 23 ++++++++++++-----------
2 files changed, 31 insertions(+), 21 deletions(-)
diff --git a/sci-biology/bowtie/bowtie-1.1.1.ebuild b/sci-biology/bowtie/bowtie-1.1.1.ebuild
index ad20591..f152518 100644
--- a/sci-biology/bowtie/bowtie-1.1.1.ebuild
+++ b/sci-biology/bowtie/bowtie-1.1.1.ebuild
@@ -4,22 +4,27 @@
EAPI=5
-inherit base eutils toolchain-funcs
+inherit eutils toolchain-funcs
DESCRIPTION="An ultrafast memory-efficient short read aligner"
HOMEPAGE="http://bowtie-bio.sourceforge.net/"
-SRC_URI="mirror://sourceforge/bowtie-bio/bowtie-1.1.1-src.zip"
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
LICENSE="Artistic"
SLOT="1"
-IUSE=""
KEYWORDS="~amd64 ~x86 ~x64-macos"
+IUSE="examples"
+
DEPEND="app-arch/unzip"
RDEPEND=""
PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch )
+src_prepare() {
+ epatch ${PATCHES[@]}
+}
+
src_compile() {
unset CFLAGS
emake \
@@ -29,14 +34,18 @@ src_compile() {
}
src_install() {
- dobin bowtie bowtie-*
- exeinto /usr/share/${PN}/scripts
- doexe scripts/*
+ dobin ${PN} ${PN}-*
- insinto /usr/share/${PN}
- doins -r genomes indexes
+ exeinto /usr/libexec/${PN}
+ doexe scripts/*
- newman MANUAL bowtie.1
+ newman MANUAL ${PN}
dodoc AUTHORS NEWS TUTORIAL doc/README
- dohtml doc/{manual.html,style.css}
+ docinto html
+ dodoc doc/{manual.html,style.css}
+
+ if use examples; then
+ insinto /usr/share/${PN}
+ doins -r genomes indexes
+ fi
}
diff --git a/sci-biology/bowtie/bowtie-2.2.4.ebuild b/sci-biology/bowtie/bowtie-2.2.4.ebuild
index 19e0bca..4b518ca 100644
--- a/sci-biology/bowtie/bowtie-2.2.4.ebuild
+++ b/sci-biology/bowtie/bowtie-2.2.4.ebuild
@@ -4,7 +4,7 @@
EAPI=5
-inherit base eutils toolchain-funcs
+inherit eutils toolchain-funcs
DESCRIPTION="An ultrafast memory-efficient short read aligner"
HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"
@@ -12,9 +12,11 @@ SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source
LICENSE="GPL-3"
SLOT="2"
-IUSE="examples"
KEYWORDS="~amd64 ~x86"
+IUSE="examples cpu_flags_x86_sse2"
+REQUIRED_USE="cpu_flags_x86_sse2"
+
RDEPEND="dev-lang/perl"
DEPEND="${RDEPEND}
app-arch/unzip"
@@ -23,16 +25,13 @@ S="${WORKDIR}/${PN}2-${PV}"
PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch )
-pkg_pretend() {
- grep "sse2" /proc/cpuinfo > /dev/null
- if [[ $? -ne 0 ]] ; then
- ewarn "Your processor does not support sse2. Bowtie will probably not work on this machine."
- fi
+src_prepare() {
+ epatch ${PATCHES[@]}
}
src_compile() {
+ unset CFLAGS
emake \
- CC="$(tc-getCC)" \
CXX="$(tc-getCXX)" \
EXTRA_FLAGS="${LDFLAGS}" \
RELEASE_FLAGS="${CXXFLAGS} -msse2"
@@ -40,12 +39,14 @@ src_compile() {
src_install() {
dobin ${PN}2 ${PN}2-*
- exeinto /usr/share/${PN}2/scripts
+
+ exeinto /usr/libexec/${PN}2
doexe scripts/*
- newman MANUAL ${PN}2.1
+ newman MANUAL ${PN}2.2
dodoc AUTHORS NEWS TUTORIAL
- dohtml doc/manual.html doc/style.css
+ docinto html
+ dodoc doc/{manual.html,style.css}
if use examples; then
insinto /usr/share/${PN}2
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
@ 2013-09-28 10:57 Justin Lecher
0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2013-09-28 10:57 UTC (permalink / raw
To: gentoo-commits
commit: 4603ef2b8bf5e03c44f59aaf2ed43ab046d6ca8f
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 28 10:56:47 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Sep 28 10:56:47 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4603ef2b
sci-biology/bowtie: Exchange common variables, fix SRC_URI
Package-Manager: portage-2.2.7
---
sci-biology/bowtie/ChangeLog | 7 +++++++
sci-biology/bowtie/bowtie-2.1.0.ebuild | 6 +++---
2 files changed, 10 insertions(+), 3 deletions(-)
diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog
new file mode 100644
index 0000000..1a636c5
--- /dev/null
+++ b/sci-biology/bowtie/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for sci-biology/bowtie
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 28 Sep 2013; Justin Lecher <jlec@gentoo.org> bowtie-2.1.0.ebuild:
+ Exchange common variables, fix SRC_URI
+
diff --git a/sci-biology/bowtie/bowtie-2.1.0.ebuild b/sci-biology/bowtie/bowtie-2.1.0.ebuild
index 26bf770..a12279a 100644
--- a/sci-biology/bowtie/bowtie-2.1.0.ebuild
+++ b/sci-biology/bowtie/bowtie-2.1.0.ebuild
@@ -8,7 +8,7 @@ inherit eutils toolchain-funcs
DESCRIPTION="An ultrafast memory-efficient short read aligner"
HOMEPAGE="http://bowtie-bio.sourceforge.net/"
-SRC_URI="mirror://sourceforge/bowtie-bio/${P}-source.zip"
+SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
LICENSE="GPL-3"
SLOT="2"
@@ -41,11 +41,11 @@ src_compile() {
}
src_install() {
- dobin bowtie2 bowtie2-*
+ dobin ${PN}2 ${PN}2-*
exeinto /usr/share/${PN}2/scripts
doexe scripts/*
- newman MANUAL bowtie2.1
+ newman MANUAL ${PN}2.1
dodoc AUTHORS NEWS TUTORIAL
dohtml doc/manual.html doc/style.css
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
@ 2013-09-27 15:05 Nicolas Bock
0 siblings, 0 replies; 17+ messages in thread
From: Nicolas Bock @ 2013-09-27 15:05 UTC (permalink / raw
To: gentoo-commits
commit: 9ee84fa74a5bc48850d98dd49edbe223e8085e5a
Author: cel <cel.gentoo <AT> gmail <DOT> com>
AuthorDate: Thu Sep 26 19:35:23 2013 +0000
Commit: Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Thu Sep 26 19:35:23 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9ee84fa7
sci-biology/bowtie: fixed check for sse2 support.
---
sci-biology/bowtie/bowtie-2.1.0.ebuild | 21 ++++++++-------------
1 file changed, 8 insertions(+), 13 deletions(-)
diff --git a/sci-biology/bowtie/bowtie-2.1.0.ebuild b/sci-biology/bowtie/bowtie-2.1.0.ebuild
index c2c5024..26bf770 100644
--- a/sci-biology/bowtie/bowtie-2.1.0.ebuild
+++ b/sci-biology/bowtie/bowtie-2.1.0.ebuild
@@ -4,7 +4,7 @@
EAPI=5
-inherit eutils flag-o-matic toolchain-funcs
+inherit eutils toolchain-funcs
DESCRIPTION="An ultrafast memory-efficient short read aligner"
HOMEPAGE="http://bowtie-bio.sourceforge.net/"
@@ -12,23 +12,19 @@ SRC_URI="mirror://sourceforge/bowtie-bio/${P}-source.zip"
LICENSE="GPL-3"
SLOT="2"
-IUSE="sse2 examples"
+IUSE="examples"
KEYWORDS="~amd64 ~x86"
-CDEPEND="dev-lang/perl"
-DEPEND="${CDEPEND} \
+RDEPEND="dev-lang/perl"
+DEPEND="${RDEPEND}
app-arch/unzip"
-RDEPEND="${CDEPEND}"
S="${WORKDIR}/${PN}2-${PV}"
pkg_pretend() {
- if ! use sse2 ; then
- ebegin
- eerror "bowtie2 requires sse2 support. Please make sure your system supports"
- eerror "sse2 and enable the sse2 use flag."
- eend
- die
+ grep "sse2" /proc/cpuinfo > /dev/null
+ if [[ $? -ne 0 ]] ; then
+ ewarn "Your processor does not support sse2. Bowtie will probably not work on this machine."
fi
}
@@ -37,12 +33,11 @@ src_prepare() {
}
src_compile() {
- use sse2 && append-cxxflags -msse2
emake \
CC="$(tc-getCC)" \
CPP="$(tc-getCXX)" \
EXTRA_FLAGS="${LDFLAGS}" \
- RELEASE_FLAGS="${CXXFLAGS}"
+ RELEASE_FLAGS="${CXXFLAGS} -msse2"
}
src_install() {
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2020-12-30 22:52 [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/ Martin Mokrejs
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2021-03-17 10:37 Andrew Ammerlaan
2021-03-16 18:15 Andrew Ammerlaan
2021-03-06 10:02 Andrew Ammerlaan
2020-02-28 23:07 Martin Mokrejs
2020-02-26 8:49 Martin Mokrejs
2019-03-25 11:21 Martin Mokrejs
2019-02-19 11:26 Martin Mokrejs
2019-02-19 11:24 Martin Mokrejs
2015-10-12 6:51 Marius Brehler
2015-10-12 6:51 Marius Brehler
2015-05-01 20:38 Martin Mokrejs
2015-04-27 11:01 Martin Mokrejs
2015-02-08 21:07 Christoph Junghans
2015-02-08 21:07 Christoph Junghans
2013-09-28 10:57 Justin Lecher
2013-09-27 15:05 Nicolas Bock
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