* [gentoo-commits] proj/sci:master commit in: sci-biology/MolBioLib/
@ 2016-04-01 19:14 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2016-04-01 19:14 UTC (permalink / raw
To: gentoo-commits
commit: efe8a4f25b66f0f3dbd800e26d8f12973330b5c8
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 1 19:11:50 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 1 19:11:50 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=efe8a4f2
sci-biology/MolBioLib: yet another package with bundled samtools, bamtools etc.
Package-Manager: portage-2.2.28
sci-biology/MolBioLib/MolBioLib-5.ebuild | 31 +++++++++++++++++++++++++++++++
sci-biology/MolBioLib/metadata.xml | 12 ++++++++++++
2 files changed, 43 insertions(+)
diff --git a/sci-biology/MolBioLib/MolBioLib-5.ebuild b/sci-biology/MolBioLib/MolBioLib-5.ebuild
new file mode 100644
index 0000000..5cb9ea2
--- /dev/null
+++ b/sci-biology/MolBioLib/MolBioLib-5.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+DESCRIPTION="C++11 framework for rapid develop and deploy of bioinformatic tasks"
+HOMEPAGE="https://sourceforge.net/projects/molbiolib"
+SRC_URI="https://sourceforge.net/projects/molbiolib/files/MolBioLib_public.version${PV}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# contains bundled samtools-0.1.18 and bamtools (pezmaster31-bamtools-d553a62) which contains jsoncpp
+# also needs app-doc/doxygen
+DEPEND="dev-lang/perl
+ sys-devel/gcc:*
+ sys-devel/clang
+ >=sci-biology/samtools-0.1.18:0
+ <sci-biology/samtools-1:0"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/MolBioLib
+
+src_compile(){
+ perl MakeAllApps.pl || die
+}
+
+# src_install() needs to be written
diff --git a/sci-biology/MolBioLib/metadata.xml b/sci-biology/MolBioLib/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/MolBioLib/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/MolBioLib/
@ 2016-04-02 10:57 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2016-04-02 10:57 UTC (permalink / raw
To: gentoo-commits
commit: 374eb76a50b69422ed18660bac0ff4954a3454ff
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 2 10:54:41 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 2 10:54:41 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=374eb76a
sci-biology/MolBioLib: does not build, contacted upstream
Package-Manager: portage-2.2.28
sci-biology/MolBioLib/MolBioLib-5.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/MolBioLib/MolBioLib-5.ebuild b/sci-biology/MolBioLib/MolBioLib-5.ebuild
index 5cb9ea2..1f7c89a 100644
--- a/sci-biology/MolBioLib/MolBioLib-5.ebuild
+++ b/sci-biology/MolBioLib/MolBioLib-5.ebuild
@@ -10,7 +10,7 @@ SRC_URI="https://sourceforge.net/projects/molbiolib/files/MolBioLib_public.versi
LICENSE="GPL-3"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="" # does not build
IUSE=""
# contains bundled samtools-0.1.18 and bamtools (pezmaster31-bamtools-d553a62) which contains jsoncpp
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/MolBioLib/
@ 2016-04-24 9:23 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2016-04-24 9:23 UTC (permalink / raw
To: gentoo-commits
commit: 3f7c207645890ae5a2c88e763374741dc542106f
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 24 09:23:43 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 24 09:23:43 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3f7c2076
sci-biology/MolBioLib: improved ebuild based on response from author
Package-Manager: portage-2.2.28
sci-biology/MolBioLib/MolBioLib-5.ebuild | 14 +++++++++++---
1 file changed, 11 insertions(+), 3 deletions(-)
diff --git a/sci-biology/MolBioLib/MolBioLib-5.ebuild b/sci-biology/MolBioLib/MolBioLib-5.ebuild
index 1f7c89a..47ce9df 100644
--- a/sci-biology/MolBioLib/MolBioLib-5.ebuild
+++ b/sci-biology/MolBioLib/MolBioLib-5.ebuild
@@ -11,7 +11,7 @@ SRC_URI="https://sourceforge.net/projects/molbiolib/files/MolBioLib_public.versi
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="" # does not build
-IUSE=""
+IUSE="doc"
# contains bundled samtools-0.1.18 and bamtools (pezmaster31-bamtools-d553a62) which contains jsoncpp
# also needs app-doc/doxygen
@@ -19,13 +19,21 @@ DEPEND="dev-lang/perl
sys-devel/gcc:*
sys-devel/clang
>=sci-biology/samtools-0.1.18:0
- <sci-biology/samtools-1:0"
+ <sci-biology/samtools-1:0
+ doc? ( app-doc/doxygen )"
RDEPEND="${DEPEND}"
S="${WORKDIR}"/MolBioLib
+src_prepare(){
+ # edit MakeAllApps.pl
+ default
+}
+
src_compile(){
perl MakeAllApps.pl || die
}
-# src_install() needs to be written
+src_install(){
+ dodoc -r docs/doxygen/*
+}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/MolBioLib/
@ 2017-03-26 14:45 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2017-03-26 14:45 UTC (permalink / raw
To: gentoo-commits
commit: 6ff346d6fa1dbfe1cca05287e7fc133529727bc3
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 26 08:50:25 2017 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar 26 08:50:25 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6ff346d6
sci-biology/MolBioLib: Add missing SLOT operator
Package-Manager: Portage-2.3.5, Repoman-2.3.2
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/MolBioLib/MolBioLib-5.ebuild | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/sci-biology/MolBioLib/MolBioLib-5.ebuild b/sci-biology/MolBioLib/MolBioLib-5.ebuild
index 6ace7f0a1..681758724 100644
--- a/sci-biology/MolBioLib/MolBioLib-5.ebuild
+++ b/sci-biology/MolBioLib/MolBioLib-5.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -14,9 +14,10 @@ IUSE="doc"
# contains bundled samtools-0.1.18 and bamtools (pezmaster31-bamtools-d553a62) which contains jsoncpp
# also needs app-doc/doxygen
-DEPEND="dev-lang/perl
+DEPEND="
+ dev-lang/perl
sys-devel/gcc:*
- sys-devel/clang
+ sys-devel/clang:*
>=sci-biology/samtools-0.1.18:0
<sci-biology/samtools-1:0
doc? ( app-doc/doxygen )"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/MolBioLib/
@ 2019-03-25 8:52 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2019-03-25 8:52 UTC (permalink / raw
To: gentoo-commits
commit: 487854338866a64efbd9ec434743f7ab7a23bccd
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 25 08:52:33 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 25 08:52:33 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=48785433
sci-biology/MolBioLib: fix RDEPEND.suspect at least
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/MolBioLib/MolBioLib-5.ebuild | 19 ++++++++++---------
1 file changed, 10 insertions(+), 9 deletions(-)
diff --git a/sci-biology/MolBioLib/MolBioLib-5.ebuild b/sci-biology/MolBioLib/MolBioLib-5.ebuild
index 681758724..ac54cfcaf 100644
--- a/sci-biology/MolBioLib/MolBioLib-5.ebuild
+++ b/sci-biology/MolBioLib/MolBioLib-5.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-DESCRIPTION="C++11 framework for rapid develop and deploy of bioinformatic tasks"
+DESCRIPTION="C++11 framework for bioinformatics tasks"
HOMEPAGE="https://sourceforge.net/projects/molbiolib"
SRC_URI="https://sourceforge.net/projects/molbiolib/files/MolBioLib_public.version${PV}.tar.gz"
@@ -12,16 +12,16 @@ SLOT="0"
KEYWORDS="" # does not build
IUSE="doc"
-# contains bundled samtools-0.1.18 and bamtools (pezmaster31-bamtools-d553a62) which contains jsoncpp
-# also needs app-doc/doxygen
+# contains bundled samtools-0.1.18 and bamtools (pezmaster31-bamtools-d553a62)
+# which contains jsoncpp, also needs app-doc/doxygen
DEPEND="
dev-lang/perl
sys-devel/gcc:*
sys-devel/clang:*
- >=sci-biology/samtools-0.1.18:0
- <sci-biology/samtools-1:0
- doc? ( app-doc/doxygen )"
+ >=sci-biology/samtools-0.1.18:0.1-legacy
+ <sci-biology/samtools-1:0.1-legacy"
RDEPEND="${DEPEND}"
+CDEPEND="doc? ( app-doc/doxygen )"
S="${WORKDIR}"/MolBioLib
@@ -35,5 +35,6 @@ src_compile(){
}
src_install(){
- dodoc -r docs/doxygen/*
+ # TODO: install the app somehow
+ use doc && dodoc -r docs/doxygen/*
}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/MolBioLib/
@ 2022-01-25 14:28 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2022-01-25 14:28 UTC (permalink / raw
To: gentoo-commits
commit: 9279bc6ea1aa560facb262a6edd02badb8d7b1d7
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 14:28:23 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 14:28:23 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9279bc6e
sci-biology/MolBioLib: drop dead package
no update since 2016
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/MolBioLib/MolBioLib-5.ebuild | 40 --------------------------------
sci-biology/MolBioLib/metadata.xml | 15 ------------
2 files changed, 55 deletions(-)
diff --git a/sci-biology/MolBioLib/MolBioLib-5.ebuild b/sci-biology/MolBioLib/MolBioLib-5.ebuild
deleted file mode 100644
index bbbbeb605..000000000
--- a/sci-biology/MolBioLib/MolBioLib-5.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DOCS_BUILDER="doxygen"
-DOCS_DEPEND="media-gfx/graphviz"
-
-inherit docs
-
-DESCRIPTION="C++11 framework for bioinformatics tasks"
-HOMEPAGE="https://sourceforge.net/projects/molbiolib"
-SRC_URI="https://sourceforge.net/projects/molbiolib/files/MolBioLib_public.version${PV}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="" # does not build
-
-# contains bundled samtools-0.1.18 and bamtools (pezmaster31-bamtools-d553a62)
-# which contains jsoncpp, also needs app-doc/doxygen
-DEPEND="
- dev-lang/perl
- sys-devel/gcc:*
- sys-devel/clang:*
- >=sci-biology/samtools-0.1.18:0.1-legacy
- <sci-biology/samtools-1:0.1-legacy"
-RDEPEND="${DEPEND}"
-CDEPEND="doc? ( app-doc/doxygen )"
-
-S="${WORKDIR}"/MolBioLib
-
-src_compile(){
- perl MakeAllApps.pl || die
- docs_compile
-}
-
-src_install() {
- einstalldocs
- # TODO: install this
-}
diff --git a/sci-biology/MolBioLib/metadata.xml b/sci-biology/MolBioLib/metadata.xml
deleted file mode 100644
index 3b9e38617..000000000
--- a/sci-biology/MolBioLib/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">molbiolib</remote-id>
- </upstream>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 6+ messages in thread
end of thread, other threads:[~2022-01-25 14:28 UTC | newest]
Thread overview: 6+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2017-03-26 14:45 [gentoo-commits] proj/sci:master commit in: sci-biology/MolBioLib/ Justin Lecher
-- strict thread matches above, loose matches on Subject: below --
2022-01-25 14:28 Andrew Ammerlaan
2019-03-25 8:52 Martin Mokrejs
2016-04-24 9:23 Martin Mokrejs
2016-04-02 10:57 Martin Mokrejs
2016-04-01 19:14 Martin Mokrejs
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox