[gentoo-commits] proj/sci:master commit in: sci-biology/MolBioLib/
commit: 9279bc6ea1aa560facb262a6edd02badb8d7b1d7
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Tue Jan 25 14:28:23 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Tue Jan 25 14:28:23 2022 +
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 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 eb605..0
--- 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
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- mmokr...@fold.natur.cuni.cz
- Martin Mokrejs
-
-
- sci-biol...@gentoo.org
- Gentoo Biology Project
-
-
- molbiolib
-
-
[gentoo-commits] proj/sci:master commit in: sci-biology/MolBioLib/, profiles/
commit: 0a3193bdb34b5d005a47c68c6f049d990be406a6
Author: Andrew Ammerlaan riseup net>
AuthorDate: Tue Jan 19 11:22:47 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Tue Jan 19 11:22:59 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0a3193bd
sci-biology/MolBioLib: fix fetching
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
profiles/package.mask| 1 -
sci-biology/MolBioLib/MolBioLib-5.ebuild | 20 ++--
2 files changed, 10 insertions(+), 11 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index 12a2d067b..c0e7743a2 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -84,4 +84,3 @@ sci-biology/manatee-igs
sci-biology/manatee-jcvi
sci-biology/mavid
sci-biology/MeV
-sci-biology/MolBioLib
diff --git a/sci-biology/MolBioLib/MolBioLib-5.ebuild
b/sci-biology/MolBioLib/MolBioLib-5.ebuild
index ac54cfcaf..eb605 100644
--- a/sci-biology/MolBioLib/MolBioLib-5.ebuild
+++ b/sci-biology/MolBioLib/MolBioLib-5.ebuild
@@ -1,8 +1,13 @@
-# Copyright 1999-2019 Gentoo Authors
+# 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;
@@ -10,7 +15,6 @@
SRC_URI="https://sourceforge.net/projects/molbiolib/files/MolBioLib_public.versi
LICENSE="GPL-3"
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
@@ -25,16 +29,12 @@ CDEPEND="doc? ( app-doc/doxygen )"
S="${WORKDIR}"/MolBioLib
-src_prepare(){
- # edit MakeAllApps.pl
- default
-}
-
src_compile(){
perl MakeAllApps.pl || die
+ docs_compile
}
-src_install(){
- # TODO: install the app somehow
- use doc && dodoc -r docs/doxygen/*
+src_install() {
+ einstalldocs
+ # TODO: install this
}
[gentoo-commits] proj/sci:master commit in: sci-biology/MolBioLib/
commit: 487854338866a64efbd9ec434743f7ab7a23bccd
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Mon Mar 25 08:52:33 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Mar 25 08:52:33 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=48785433
sci-biology/MolBioLib: fix RDEPEND.suspect at least
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/MolBioLib/MolBioLib-5.ebuild | 19 ++-
1 file changed, 10 insertions(+), 9 deletions(-)
diff --git a/sci-biology/MolBioLib/MolBioLib-5.ebuild
b/sci-biology/MolBioLib/MolBioLib-5.ebuild
index 681758724..ac54cfcaf 100644
--- a/sci-biology/MolBioLib/MolBioLib-5.ebuild
+++ b/sci-biology/MolBioLib/MolBioLib-5.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-DESCRIPTION="C++11 framework for rapid develop and deploy of bioinformatic
tasks"
+DESCRIPTION="C++11 framework for bioinformatics tasks"
HOMEPAGE="https://sourceforge.net/projects/molbiolib;
SRC_URI="https://sourceforge.net/projects/molbiolib/files/MolBioLib_public.version${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-0.1.18:0.1-legacy
+
[gentoo-commits] proj/sci:master commit in: sci-biology/MolBioLib/
commit: 6ff346d6fa1dbfe1cca05287e7fc133529727bc3 Author: Justin Lecher gentoo org> AuthorDate: Sun Mar 26 08:50:25 2017 + Commit: Justin Lecher gentoo org> CommitDate: Sun Mar 26 08:50:25 2017 + 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 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
[gentoo-commits] proj/sci:master commit in: sci-biology/MolBioLib/
commit: 3f7c207645890ae5a2c88e763374741dc542106f Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Sun Apr 24 09:23:43 2016 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sun Apr 24 09:23:43 2016 + 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 -
[gentoo-commits] proj/sci:master commit in: sci-biology/MolBioLib/
commit: 374eb76a50b69422ed18660bac0ff4954a3454ff Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Sat Apr 2 10:54:41 2016 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sat Apr 2 10:54:41 2016 + 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
[gentoo-commits] proj/sci:master commit in: sci-biology/MolBioLib/
commit: efe8a4f25b66f0f3dbd800e26d8f12973330b5c8
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Apr 1 19:11:50 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Apr 1 19:11:50 2016 +
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 000..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
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
+sci-biol...@gentoo.org
+Gentoo Biology Project
+
+
