* [gentoo-commits] proj/sci:master commit in: sci-biology/VelvetOptimiser/
@ 2014-04-15 9:27 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2014-04-15 9:27 UTC (permalink / raw
To: gentoo-commits
commit: 36271ba96f6900f3219ae9606d6a3757ce21fbd7
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Apr 15 09:25:33 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Apr 15 09:25:33 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=36271ba9
sci-biology/VelvetOptimiser: new package
Package-Manager: portage-2.2.7
---
sci-biology/VelvetOptimiser/ChangeLog | 9 +++++++
.../VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild | 29 ++++++++++++++++++++++
sci-biology/VelvetOptimiser/metadata.xml | 9 +++++++
3 files changed, 47 insertions(+)
diff --git a/sci-biology/VelvetOptimiser/ChangeLog b/sci-biology/VelvetOptimiser/ChangeLog
new file mode 100644
index 0000000..573bfac
--- /dev/null
+++ b/sci-biology/VelvetOptimiser/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/VelvetOptimiser
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*VelvetOptimiser-2.2.5 (15 Apr 2014)
+
+ 15 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +VelvetOptimiser-2.2.5.ebuild, +metadata.xml:
+ sci-biology/VelvetOptimiser: new package
diff --git a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
new file mode 100644
index 0000000..1491603
--- /dev/null
+++ b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit perl-module
+
+DESCRIPTION="Optimise three primary parameter options (K, -exp_cov, -cov_cutoff) for Velvet sequence assembler."
+HOMEPAGE="http://www.vicbioinformatics.com/software.velvetoptimiser.shtml"
+SRC_URI="http://www.vicbioinformatics.com/"${P}".tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ >=sci-biology/bioperl-1.4
+ >=sci-biology/velvet-0.7.5.1
+ >=dev-lang/perl-5.8"
+
+src_install(){
+ dobin VelvetOptimiser.pl
+ insinto ${VENDOR_LIB}/${PN}
+ doins VelvetOpt/*.pm
+ dodoc README INSTALL CHANGELOG || die
+}
diff --git a/sci-biology/VelvetOptimiser/metadata.xml b/sci-biology/VelvetOptimiser/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/VelvetOptimiser/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] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/VelvetOptimiser/
@ 2014-04-15 9:36 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2014-04-15 9:36 UTC (permalink / raw
To: gentoo-commits
commit: 9cb8f542b9224a22e836a8b6fa6a6b3713adda18
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Apr 15 09:34:29 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Apr 15 09:34:29 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9cb8f542
sci-biology/VelvetOptimiser: add requirement for threaded perl
Package-Manager: portage-2.2.7
---
sci-biology/VelvetOptimiser/ChangeLog | 4 ++++
sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild | 2 +-
2 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/sci-biology/VelvetOptimiser/ChangeLog b/sci-biology/VelvetOptimiser/ChangeLog
index 573bfac..44fa73b 100644
--- a/sci-biology/VelvetOptimiser/ChangeLog
+++ b/sci-biology/VelvetOptimiser/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 15 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ VelvetOptimiser-2.2.5.ebuild:
+ sci-biology/VelvetOptimiser: add requirement for threaded perl
+
*VelvetOptimiser-2.2.5 (15 Apr 2014)
15 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
index 1491603..1be9973 100644
--- a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
+++ b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
@@ -19,7 +19,7 @@ DEPEND=""
RDEPEND="${DEPEND}
>=sci-biology/bioperl-1.4
>=sci-biology/velvet-0.7.5.1
- >=dev-lang/perl-5.8"
+ >=dev-lang/perl-5.8[ithreads]"
src_install(){
dobin VelvetOptimiser.pl
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/VelvetOptimiser/
@ 2014-06-27 7:51 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2014-06-27 7:51 UTC (permalink / raw
To: gentoo-commits
commit: 1d678377b2ad764c6ef12669ca6f9a8e637cf408
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jun 27 07:50:25 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jun 27 07:50:25 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1d678377
sci-biology/VelevtOptimiser: dropping perl version requirement as I am unbale to check for >=5.8 but make sure 5.16 evaluates as True
---
sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
index 1be9973..55290bc 100644
--- a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
+++ b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
@@ -19,7 +19,7 @@ DEPEND=""
RDEPEND="${DEPEND}
>=sci-biology/bioperl-1.4
>=sci-biology/velvet-0.7.5.1
- >=dev-lang/perl-5.8[ithreads]"
+ dev-lang/perl[ithreads]" # actually >=5.8 but make sure 5.16 is recognized as > 5.8, heh
src_install(){
dobin VelvetOptimiser.pl
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/VelvetOptimiser/
@ 2015-04-17 23:56 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2015-04-17 23:56 UTC (permalink / raw
To: gentoo-commits
commit: 3aed7feaab0513623e25c1cedbb7f8284c86ba6d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 17 23:54:14 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 17 23:54:14 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3aed7fea
sci-biology/VelvetOptimiser: fixed installation of perl-related files
Package-Manager: portage-2.2.18
sci-biology/VelvetOptimiser/ChangeLog | 6 +++++-
sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild | 10 ++++++----
2 files changed, 11 insertions(+), 5 deletions(-)
diff --git a/sci-biology/VelvetOptimiser/ChangeLog b/sci-biology/VelvetOptimiser/ChangeLog
index 44fa73b..6c91c0b 100644
--- a/sci-biology/VelvetOptimiser/ChangeLog
+++ b/sci-biology/VelvetOptimiser/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/VelvetOptimiser
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ VelvetOptimiser-2.2.5.ebuild:
+ sci-biology/VelvetOptimiser: fixed installation of perl-related files
+
15 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
VelvetOptimiser-2.2.5.ebuild:
sci-biology/VelvetOptimiser: add requirement for threaded perl
diff --git a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
index 55290bc..69a7bd0 100644
--- a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
+++ b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
@@ -1,10 +1,11 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=5
-inherit perl-module
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module eutils
DESCRIPTION="Optimise three primary parameter options (K, -exp_cov, -cov_cutoff) for Velvet sequence assembler."
HOMEPAGE="http://www.vicbioinformatics.com/software.velvetoptimiser.shtml"
@@ -23,7 +24,8 @@ RDEPEND="${DEPEND}
src_install(){
dobin VelvetOptimiser.pl
- insinto ${VENDOR_LIB}/${PN}
+ perl_set_version
+ insinto ${VENDOR_LIB}/VelvetOpt
doins VelvetOpt/*.pm
- dodoc README INSTALL CHANGELOG || die
+ dodoc README INSTALL CHANGELOG
}
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/VelvetOptimiser/
@ 2017-01-29 20:25 Justin Lecher
0 siblings, 0 replies; 8+ messages in thread
From: Justin Lecher @ 2017-01-29 20:25 UTC (permalink / raw
To: gentoo-commits
commit: 4a583377fcfe0d53077af7c0ee0c9991ff4d6c84
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 29 20:22:31 2017 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan 29 20:25:16 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4a583377
sci-biology/VelvetOptimiser: QA fixes
Bump to EAPI 6
shorten DESCRIPTION
Move to perl-functions.eclass
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild | 9 ++++-----
sci-biology/VelvetOptimiser/metadata.xml | 2 +-
2 files changed, 5 insertions(+), 6 deletions(-)
diff --git a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
index b7a1bcb..923aaa8 100644
--- a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
+++ b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
@@ -1,13 +1,12 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils
+inherit perl-functions
-DESCRIPTION="Optimise three primary parameter options (K, -exp_cov, -cov_cutoff) for Velvet sequence assembler"
+DESCRIPTION="Optimise Velvet sequence assembler"
HOMEPAGE="http://www.vicbioinformatics.com/software.velvetoptimiser.shtml"
SRC_URI="http://www.vicbioinformatics.com/"${P}".tar.gz"
diff --git a/sci-biology/VelvetOptimiser/metadata.xml b/sci-biology/VelvetOptimiser/metadata.xml
index 1699e58..f68a1b6 100644
--- a/sci-biology/VelvetOptimiser/metadata.xml
+++ b/sci-biology/VelvetOptimiser/metadata.xml
@@ -5,7 +5,7 @@
<email>mmokrejs@fold.natur.cuni.cz</email>
<name>Martin Mokrejs</name>
</maintainer>
-<maintainer type="project">
+ <maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/VelvetOptimiser/
@ 2021-01-18 12:53 Andrew Ammerlaan
0 siblings, 0 replies; 8+ messages in thread
From: Andrew Ammerlaan @ 2021-01-18 12:53 UTC (permalink / raw
To: gentoo-commits
commit: 538fa4471cb85c2a2e2c2ddfa47f423a7690414a
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 12:52:56 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 12:52:56 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=538fa447
sci-biology/VelvetOptimiser: version bump 2.2.6, fetching fixed
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
...Optimiser-2.2.5.ebuild => VelvetOptimiser-2.2.6.ebuild} | 14 ++++++--------
1 file changed, 6 insertions(+), 8 deletions(-)
diff --git a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild
similarity index 64%
rename from sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
rename to sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild
index f5ad6e636..e000e6290 100644
--- a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
+++ b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild
@@ -1,21 +1,19 @@
-# 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 perl-functions
DESCRIPTION="Optimise Velvet sequence assembler"
-HOMEPAGE="http://www.vicbioinformatics.com/software.velvetoptimiser.shtml"
-SRC_URI="http://www.vicbioinformatics.com/"${P}".tar.gz"
+HOMEPAGE="https://vicbioinformatics.com/software.velvetoptimiser.shtml"
+SRC_URI="https://github.com/tseemann/VelvetOptimiser/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64"
-IUSE=""
-DEPEND=""
-RDEPEND="${DEPEND}
+RDEPEND="
>=sci-biology/bioperl-1.4
>=sci-biology/velvet-0.7.5.1
dev-lang/perl[ithreads]" # actually >=5.8 but make sure 5.16 is recognized as > 5.8, heh
@@ -25,5 +23,5 @@ src_install(){
perl_set_version
insinto ${VENDOR_LIB}/VelvetOpt
doins VelvetOpt/*.pm
- dodoc README INSTALL CHANGELOG
+ einstalldocs
}
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/VelvetOptimiser/
@ 2021-03-18 18:54 Andrew Ammerlaan
0 siblings, 0 replies; 8+ messages in thread
From: Andrew Ammerlaan @ 2021-03-18 18:54 UTC (permalink / raw
To: gentoo-commits
commit: 023c0679b9c5aba5309da72cecea35fae5ef9364
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Mar 18 18:44:48 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Mar 18 18:44:48 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=023c0679
sci-biology/VelvetOptimiser: use perl_domodule
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild
index e000e6290..49f2b6d9f 100644
--- a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild
+++ b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild
@@ -21,7 +21,6 @@ RDEPEND="
src_install(){
dobin VelvetOptimiser.pl
perl_set_version
- insinto ${VENDOR_LIB}/VelvetOpt
- doins VelvetOpt/*.pm
+ perl_domodule VelvetOpt/*.pm
einstalldocs
}
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/VelvetOptimiser/
@ 2024-05-22 15:57 Andrew Ammerlaan
0 siblings, 0 replies; 8+ messages in thread
From: Andrew Ammerlaan @ 2024-05-22 15:57 UTC (permalink / raw
To: gentoo-commits
commit: e120252601caa45b738cfc059a709d5d9ab9ec67
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Wed May 22 15:56:52 2024 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Wed May 22 15:56:52 2024 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e1202526
sci-biology/VelvetOptimiser: fix dependency on perl
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild
index 49f2b6d9f..096349f5a 100644
--- a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild
+++ b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild
@@ -16,7 +16,7 @@ KEYWORDS="~amd64"
RDEPEND="
>=sci-biology/bioperl-1.4
>=sci-biology/velvet-0.7.5.1
- dev-lang/perl[ithreads]" # actually >=5.8 but make sure 5.16 is recognized as > 5.8, heh
+ dev-lang/perl[perl_features_ithreads]" # actually >=5.8 but make sure 5.16 is recognized as > 5.8, heh
src_install(){
dobin VelvetOptimiser.pl
^ permalink raw reply related [flat|nested] 8+ messages in thread
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