* [gentoo-commits] proj/sci:master commit in: sci-biology/flexbar/
@ 2014-03-23 16:34 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2014-03-23 16:34 UTC (permalink / raw
To: gentoo-commits
commit: 53562c6fe46a84363a92dca87a7e4e4c6f78f77f
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 16:33:19 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 16:33:19 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=53562c6f
sci-biology/flexbar: new package, needs >=sci-biology/seqan-1.4.1 to appear first in the tree
Package-Manager: portage-2.2.7
---
sci-biology/flexbar/ChangeLog | 10 ++++++++++
sci-biology/flexbar/flexbar-2.4.ebuild | 23 +++++++++++++++++++++++
sci-biology/flexbar/metadata.xml | 9 +++++++++
3 files changed, 42 insertions(+)
diff --git a/sci-biology/flexbar/ChangeLog b/sci-biology/flexbar/ChangeLog
new file mode 100644
index 0000000..371eef0
--- /dev/null
+++ b/sci-biology/flexbar/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/flexbar
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*flexbar-2.4 (23 Mar 2014)
+
+ 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +flexbar-2.4.ebuild,
+ +metadata.xml:
+ sci-biology/flexbar: new package, needs >=sci-biology/seqan-1.4.1 to appear
+ first in the tree
diff --git a/sci-biology/flexbar/flexbar-2.4.ebuild b/sci-biology/flexbar/flexbar-2.4.ebuild
new file mode 100644
index 0000000..5b65338
--- /dev/null
+++ b/sci-biology/flexbar/flexbar-2.4.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit cmake-utils
+
+DESCRIPTION="Barcode, MID tag and adapter sequence removal"
+HOMEPAGE="https://sourceforge.net/p/flexbar/wiki/Manual"
+SRC_URI="http://sourceforge.net/projects/flexbar/files/2.4/flexbar_v2.4_src.tgz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+CDEPEND="dev-cpp/tbb
+ >=sci-biology/seqan-1.4.1"
+DEPEND="${CDEPEND}"
+RDEPEND="${CDEPEND}"
+
+S="${WORKDIR}"/"${PN}"_v"${PV}"_src
diff --git a/sci-biology/flexbar/metadata.xml b/sci-biology/flexbar/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/flexbar/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/flexbar/
@ 2017-01-29 14:20 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2017-01-29 14:20 UTC (permalink / raw
To: gentoo-commits
commit: 7ede6a900846d17f08c7b9f62238b0a810b1b49f
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 29 14:04:17 2017 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan 29 14:04:17 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7ede6a90
sci-biology/flexbar: QA fixes
Bump to6 EAPI
add missing slot operator
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/flexbar/flexbar-2.4.ebuild | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/sci-biology/flexbar/flexbar-2.4.ebuild b/sci-biology/flexbar/flexbar-2.4.ebuild
index bcbe2c3..a096164 100644
--- a/sci-biology/flexbar/flexbar-2.4.ebuild
+++ b/sci-biology/flexbar/flexbar-2.4.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
inherit cmake-utils
@@ -15,8 +15,9 @@ SLOT="0"
KEYWORDS=""
IUSE=""
-CDEPEND="dev-cpp/tbb
- >=sci-biology/seqan-1.4.1"
+CDEPEND="
+ dev-cpp/tbb
+ >=sci-biology/seqan-1.4.1:0"
DEPEND="${CDEPEND}"
RDEPEND="${CDEPEND}"
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/flexbar/
@ 2017-02-26 13:52 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2017-02-26 13:52 UTC (permalink / raw
To: gentoo-commits
commit: 26242100ae861907ae58864ffac9163bf9be51ed
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Feb 26 13:52:38 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Feb 26 13:52:38 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=26242100
sci-biology/flexbar: version bump
https://github.com/seqan/flexbar/issues/8
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/flexbar/flexbar-2.4.ebuild | 23 ----------------------
sci-biology/flexbar/flexbar-2.7.0.ebuild | 33 ++++++++++++++++++++++++++++++++
2 files changed, 33 insertions(+), 23 deletions(-)
diff --git a/sci-biology/flexbar/flexbar-2.4.ebuild b/sci-biology/flexbar/flexbar-2.4.ebuild
deleted file mode 100644
index 515dabcfc..000000000
--- a/sci-biology/flexbar/flexbar-2.4.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-DESCRIPTION="Barcode, MID tag and adapter sequence removal"
-HOMEPAGE="https://sourceforge.net/p/flexbar/wiki/Manual"
-SRC_URI="http://sourceforge.net/projects/flexbar/files/2.4/flexbar_v2.4_src.tgz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-CDEPEND="
- dev-cpp/tbb
- >=sci-biology/seqan-1.4.1:0"
-DEPEND="${CDEPEND}"
-RDEPEND="${CDEPEND}"
-
-S="${WORKDIR}"/"${PN}"_v"${PV}"_src
diff --git a/sci-biology/flexbar/flexbar-2.7.0.ebuild b/sci-biology/flexbar/flexbar-2.7.0.ebuild
new file mode 100644
index 000000000..5fbee3998
--- /dev/null
+++ b/sci-biology/flexbar/flexbar-2.7.0.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit cmake-utils
+
+DESCRIPTION="Barcode, MID tag and adapter sequence removal"
+HOMEPAGE="https://github.com/seqan/flexbar"
+SRC_URI="https://github.com/seqan/flexbar/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+CDEPEND="
+ dev-cpp/tbb
+ >=sci-biology/seqan-2.1.1:0"
+DEPEND="${CDEPEND}"
+RDEPEND="${CDEPEND}"
+
+# TODO: need to call 'pkg-config --cflags seqan-2.2' and pass it down
+src_configure() {
+ local CPPFLAGS=${CPPFLAGS}
+ append-cppflags `pkg-config --cflags seqan-2.2`
+ local CXXFLAGS="${CXXFLAGS}"
+ append-cxxflags "-std=c++14"
+ cmake-utils_src_configure
+}
+
+# SeqAn requires C++14! You must compile your application with -std=c++14, -std=gnu++14 or -std=c++1y
+# https://github.com/seqan/flexbar/issues/8
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/flexbar/
@ 2017-02-26 13:56 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2017-02-26 13:56 UTC (permalink / raw
To: gentoo-commits
commit: c97422a68682ca78715b64e14bf27e45e6dc45e3
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Feb 26 13:56:34 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Feb 26 13:56:34 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c97422a6
sci-biology/flexbar: remove spaces
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/flexbar/flexbar-2.7.0.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/flexbar/flexbar-2.7.0.ebuild b/sci-biology/flexbar/flexbar-2.7.0.ebuild
index 5fbee3998..9fc465c10 100644
--- a/sci-biology/flexbar/flexbar-2.7.0.ebuild
+++ b/sci-biology/flexbar/flexbar-2.7.0.ebuild
@@ -23,7 +23,7 @@ RDEPEND="${CDEPEND}"
# TODO: need to call 'pkg-config --cflags seqan-2.2' and pass it down
src_configure() {
local CPPFLAGS=${CPPFLAGS}
- append-cppflags `pkg-config --cflags seqan-2.2`
+ append-cppflags `pkg-config --cflags seqan-2.2`
local CXXFLAGS="${CXXFLAGS}"
append-cxxflags "-std=c++14"
cmake-utils_src_configure
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/flexbar/
@ 2017-04-15 0:12 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2017-04-15 0:12 UTC (permalink / raw
To: gentoo-commits
commit: dd7e564441676f8fbce36c262cb15aa865f5b545
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 15 00:11:55 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 15 00:11:55 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=dd7e5644
sci-biology/flexbar: version bump, added KEYWORDS
We still could filter away '-Wl,-O1' from CXXFLAGS.
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/flexbar/flexbar-3.0.0.ebuild | 41 ++++++++++++++++++++++++++++++++
1 file changed, 41 insertions(+)
diff --git a/sci-biology/flexbar/flexbar-3.0.0.ebuild b/sci-biology/flexbar/flexbar-3.0.0.ebuild
new file mode 100644
index 000000000..65f5dd077
--- /dev/null
+++ b/sci-biology/flexbar/flexbar-3.0.0.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit cmake-utils
+
+DESCRIPTION="Barcode, MID tag and adapter sequence removal"
+HOMEPAGE="https://github.com/seqan/flexbar"
+SRC_URI="https://github.com/seqan/flexbar/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+CDEPEND="
+ dev-cpp/tbb
+ >=sci-biology/seqan-2.1.1:0
+ sys-libs/zlib
+ app-arch/bzip2"
+DEPEND="${CDEPEND}"
+RDEPEND="${CDEPEND}"
+
+# TODO: need to call 'pkg-config --cflags seqan-2.2' and pass it down
+src_configure() {
+ local CPPFLAGS=${CPPFLAGS}
+ append-cppflags `pkg-config --cflags seqan-2.2`
+ local CXXFLAGS="${CXXFLAGS}"
+ append-cxxflags "-std=c++14"
+ cmake-utils_src_configure
+}
+
+# SeqAn requires C++14! You must compile your application with -std=c++14, -std=gnu++14 or -std=c++1y
+# https://github.com/seqan/flexbar/issues/8
+
+src_install(){
+ elog `pwd`
+ dobin ../"${P}"_build/flexbar
+ dodoc ../"${P}"/README.md
+}
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/flexbar/
@ 2021-01-24 14:29 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-01-24 14:29 UTC (permalink / raw
To: gentoo-commits
commit: e4d160b889b5217e7eff07576ce4df910ff2200a
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 24 14:29:33 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 24 14:29:33 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e4d160b8
sci-biology/flexbar: version bump, cmake-utils --> cmake
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/flexbar/flexbar-2.7.0.ebuild | 33 ----------------------
.../{flexbar-3.0.0.ebuild => flexbar-3.5.0.ebuild} | 10 +++----
2 files changed, 4 insertions(+), 39 deletions(-)
diff --git a/sci-biology/flexbar/flexbar-2.7.0.ebuild b/sci-biology/flexbar/flexbar-2.7.0.ebuild
deleted file mode 100644
index 9fc465c10..000000000
--- a/sci-biology/flexbar/flexbar-2.7.0.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-DESCRIPTION="Barcode, MID tag and adapter sequence removal"
-HOMEPAGE="https://github.com/seqan/flexbar"
-SRC_URI="https://github.com/seqan/flexbar/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-CDEPEND="
- dev-cpp/tbb
- >=sci-biology/seqan-2.1.1:0"
-DEPEND="${CDEPEND}"
-RDEPEND="${CDEPEND}"
-
-# TODO: need to call 'pkg-config --cflags seqan-2.2' and pass it down
-src_configure() {
- local CPPFLAGS=${CPPFLAGS}
- append-cppflags `pkg-config --cflags seqan-2.2`
- local CXXFLAGS="${CXXFLAGS}"
- append-cxxflags "-std=c++14"
- cmake-utils_src_configure
-}
-
-# SeqAn requires C++14! You must compile your application with -std=c++14, -std=gnu++14 or -std=c++1y
-# https://github.com/seqan/flexbar/issues/8
diff --git a/sci-biology/flexbar/flexbar-3.0.0.ebuild b/sci-biology/flexbar/flexbar-3.5.0.ebuild
similarity index 88%
rename from sci-biology/flexbar/flexbar-3.0.0.ebuild
rename to sci-biology/flexbar/flexbar-3.5.0.ebuild
index 65f5dd077..b390f5056 100644
--- a/sci-biology/flexbar/flexbar-3.0.0.ebuild
+++ b/sci-biology/flexbar/flexbar-3.5.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-inherit cmake-utils
+inherit cmake
DESCRIPTION="Barcode, MID tag and adapter sequence removal"
HOMEPAGE="https://github.com/seqan/flexbar"
@@ -12,7 +12,6 @@ SRC_URI="https://github.com/seqan/flexbar/archive/v${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE=""
CDEPEND="
dev-cpp/tbb
@@ -28,14 +27,13 @@ src_configure() {
append-cppflags `pkg-config --cflags seqan-2.2`
local CXXFLAGS="${CXXFLAGS}"
append-cxxflags "-std=c++14"
- cmake-utils_src_configure
+ cmake_src_configure
}
# SeqAn requires C++14! You must compile your application with -std=c++14, -std=gnu++14 or -std=c++1y
# https://github.com/seqan/flexbar/issues/8
src_install(){
- elog `pwd`
dobin ../"${P}"_build/flexbar
dodoc ../"${P}"/README.md
}
^ permalink raw reply related [flat|nested] 6+ messages in thread
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2021-01-24 14:29 Andrew Ammerlaan
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