* [gentoo-commits] proj/sci:master commit in: sci-biology/BRAKER/
@ 2015-04-27 11:39 Martin Mokrejs
0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2015-04-27 11:39 UTC (permalink / raw
To: gentoo-commits
commit: aa013962dcd3a5c45b467c96cda43c4bd8e33fad
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Apr 27 11:38:58 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Apr 27 11:38:58 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=aa013962
sci-biology/BRAKER: new package; somehow RDEPENDs are installed wrongly: Can't locate Scalar/Util/Numeric.pm in @INC (you may need to install the Scalar::Util::Numeric module)
Package-Manager: portage-2.2.18
sci-biology/BRAKER/BRAKER-20150330.ebuild | 32 +++++++++++++++++++++++++++++++
sci-biology/BRAKER/ChangeLog | 11 +++++++++++
sci-biology/BRAKER/metadata.xml | 9 +++++++++
3 files changed, 52 insertions(+)
diff --git a/sci-biology/BRAKER/BRAKER-20150330.ebuild b/sci-biology/BRAKER/BRAKER-20150330.ebuild
new file mode 100644
index 0000000..9ee5465
--- /dev/null
+++ b/sci-biology/BRAKER/BRAKER-20150330.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module
+
+DESCRIPTION="Gene prediction based on RNA-Seq using GeneMark-ET and AUGUSTUS"
+# http://bioinf.uni-greifswald.de/bioinf/publications/pag2015.pdf
+HOMEPAGE="http://bioinf.uni-greifswald.de/augustus/downloads"
+SRC_URI=" http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ virtual/perl-Scalar-List-Utils"
+
+S="${WORKDIR}"
+
+src_install(){
+ perl_set_version
+ dobin *.pl
+ insinto ${VENDOR_LIB}/${PN}
+ doins *.pm
+ dodoc README.braker
+}
diff --git a/sci-biology/BRAKER/ChangeLog b/sci-biology/BRAKER/ChangeLog
new file mode 100644
index 0000000..0a1fbb2
--- /dev/null
+++ b/sci-biology/BRAKER/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/BRAKER
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*BRAKER-20150330 (27 Apr 2015)
+
+ 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +BRAKER-20150330.ebuild, +metadata.xml:
+ sci-biology/BRAKER: new package; somehow RDEPENDs are installed wrongly: Can't
+ locate Scalar/Util/Numeric.pm in @INC (you may need to install the
+ Scalar::Util::Numeric module)
diff --git a/sci-biology/BRAKER/metadata.xml b/sci-biology/BRAKER/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/BRAKER/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] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/BRAKER/
@ 2015-04-27 18:30 Martin Mokrejs
0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2015-04-27 18:30 UTC (permalink / raw
To: gentoo-commits
commit: 03b89a8b4872d92052038aab0a9f64d7bc13c65a
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Apr 27 18:30:06 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Apr 27 18:30:06 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=03b89a8b
sci-biology/BRAKER: added a note about perl-core/Scalar-List-Utils blocking virtual/perl-Scalar-List-Utils (huh?)
Package-Manager: portage-2.2.18
sci-biology/BRAKER/BRAKER-20150330.ebuild | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/sci-biology/BRAKER/BRAKER-20150330.ebuild b/sci-biology/BRAKER/BRAKER-20150330.ebuild
index 9ee5465..63fe5f1 100644
--- a/sci-biology/BRAKER/BRAKER-20150330.ebuild
+++ b/sci-biology/BRAKER/BRAKER-20150330.ebuild
@@ -20,6 +20,10 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
virtual/perl-Scalar-List-Utils"
+#
+# BUG:
+# this causes:
+# [blocks B ] <perl-core/Scalar-List-Utils-1.380.0 ("<perl-core/Scalar-List-Utils-1.380.0" is blocking virtual/perl-Scalar-List-Utils-1.380.0)
S="${WORKDIR}"
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/BRAKER/
@ 2016-02-27 20:41 Martin Mokrejs
0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2016-02-27 20:41 UTC (permalink / raw
To: gentoo-commits
commit: 44918a4a9d9844c8d805694864e978e2c5306eec
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Feb 27 20:38:11 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Feb 27 20:38:11 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=44918a4a
sci-biology/BRAKER: version bump; update to a new LICENSE; update HOMEPAGE and SRC_URI
Package-Manager: portage-2.2.26
.../BRAKER/{BRAKER-20150330.ebuild => BRAKER-1.8.ebuild} | 16 +++++++++++-----
1 file changed, 11 insertions(+), 5 deletions(-)
diff --git a/sci-biology/BRAKER/BRAKER-20150330.ebuild b/sci-biology/BRAKER/BRAKER-1.8.ebuild
similarity index 55%
rename from sci-biology/BRAKER/BRAKER-20150330.ebuild
rename to sci-biology/BRAKER/BRAKER-1.8.ebuild
index a6ae578..ca09108 100644
--- a/sci-biology/BRAKER/BRAKER-20150330.ebuild
+++ b/sci-biology/BRAKER/BRAKER-1.8.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -9,17 +9,23 @@ inherit perl-module
DESCRIPTION="Gene prediction based on RNA-Seq using GeneMark-ET and AUGUSTUS"
# http://bioinf.uni-greifswald.de/bioinf/publications/pag2015.pdf
-HOMEPAGE="http://bioinf.uni-greifswald.de/augustus/downloads"
-SRC_URI=" http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1.tar.gz -> ${P}.tar.gz"
+HOMEPAGE="http://bioinf.uni-greifswald.de/bioinf/braker
+ http://bioinf.uni-greifswald.de/augustus/downloads"
+SRC_URI=" http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1_v"${PV}".tar.gz -> ${P}.tar.gz"
+# Download BRAKER1 from http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1.tar.gz.
+# The most recent release is version 1.8, from December 15th 2015.
+# Example data for testing the BRAKER1 pipeline is available at
+# http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1examples.tar.gz (1.1 GB).
-LICENSE="Artistic"
+LICENSE="GPL-3"
SLOT="0"
KEYWORDS=""
IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
- virtual/perl-Scalar-List-Utils"
+ virtual/perl-Scalar-List-Utils
+ sci-biology/augustus"
#
# BUG:
# this causes:
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/BRAKER/
@ 2016-02-27 20:48 Martin Mokrejs
0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2016-02-27 20:48 UTC (permalink / raw
To: gentoo-commits
commit: 0c868df8f4ba2220ce6b98584c94e23870f0e308
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Feb 27 20:45:25 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Feb 27 20:45:25 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0c868df8
sci-biology/BRAKER: add einfo referring to GeneMark-ET requirement
Package-Manager: portage-2.2.26
sci-biology/BRAKER/BRAKER-1.8.ebuild | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/sci-biology/BRAKER/BRAKER-1.8.ebuild b/sci-biology/BRAKER/BRAKER-1.8.ebuild
index ca09108..11fe269 100644
--- a/sci-biology/BRAKER/BRAKER-1.8.ebuild
+++ b/sci-biology/BRAKER/BRAKER-1.8.ebuild
@@ -26,6 +26,8 @@ DEPEND=""
RDEPEND="${DEPEND}
virtual/perl-Scalar-List-Utils
sci-biology/augustus"
+# Current version of BRAKER1 1.8 requires GeneMark-ET v.4.29 (or up).
+
#
# BUG:
# this causes:
@@ -40,3 +42,8 @@ src_install(){
doins *.pm
dodoc README.braker
}
+
+pkg_postinst(){
+ einfo "Please install GeneMark-ET >= v.4.29 after obtaininig a license from"
+ einfo "http://exon.gatech.edu/GeneMark/gmes_instructions.html"
+}
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/BRAKER/
@ 2016-07-01 10:28 Martin Mokrejs
0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2016-07-01 10:28 UTC (permalink / raw
To: gentoo-commits
commit: c619dfb295649b810b3534ebb55ff5c69ed74482
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 1 10:28:17 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 1 10:28:17 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c619dfb2
sci-biology/BRAKER: fix S
Package-Manager: portage-2.2.28
sci-biology/BRAKER/BRAKER-1.8.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/BRAKER/BRAKER-1.8.ebuild b/sci-biology/BRAKER/BRAKER-1.8.ebuild
index 11fe269..ebf7e28 100644
--- a/sci-biology/BRAKER/BRAKER-1.8.ebuild
+++ b/sci-biology/BRAKER/BRAKER-1.8.ebuild
@@ -33,7 +33,7 @@ RDEPEND="${DEPEND}
# this causes:
# [blocks B ] <perl-core/Scalar-List-Utils-1.380.0 ("<perl-core/Scalar-List-Utils-1.380.0" is blocking virtual/perl-Scalar-List-Utils-1.380.0)
-S="${WORKDIR}"
+S="${WORKDIR}"/BRAKER_v"${PV}"
src_install(){
perl_set_version
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/BRAKER/
@ 2016-07-01 10:40 Martin Mokrejs
0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2016-07-01 10:40 UTC (permalink / raw
To: gentoo-commits
commit: 51cbdef2f5cdf735664fb3869a98c63e31d96078
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 1 10:40:17 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 1 10:40:17 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=51cbdef2
sci-biology/BRAKER: fix DEPENDency on dev-perl/Scalar-Util-Numeric
Package-Manager: portage-2.2.28
sci-biology/BRAKER/BRAKER-1.8.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/BRAKER/BRAKER-1.8.ebuild b/sci-biology/BRAKER/BRAKER-1.8.ebuild
index ebf7e28..208b741 100644
--- a/sci-biology/BRAKER/BRAKER-1.8.ebuild
+++ b/sci-biology/BRAKER/BRAKER-1.8.ebuild
@@ -24,7 +24,7 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
- virtual/perl-Scalar-List-Utils
+ dev-perl/Scalar-Util-Numeric
sci-biology/augustus"
# Current version of BRAKER1 1.8 requires GeneMark-ET v.4.29 (or up).
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/BRAKER/
@ 2016-07-01 10:46 Martin Mokrejs
0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2016-07-01 10:46 UTC (permalink / raw
To: gentoo-commits
commit: a87311f012ae7f20a57d4302b78456e15fa2b600
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 1 10:46:11 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 1 10:46:11 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a87311f0
sci-biology/BRAKER: fix PERL5INC
Package-Manager: portage-2.2.28
sci-biology/BRAKER/BRAKER-1.8.ebuild | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/sci-biology/BRAKER/BRAKER-1.8.ebuild b/sci-biology/BRAKER/BRAKER-1.8.ebuild
index 208b741..439b5c2 100644
--- a/sci-biology/BRAKER/BRAKER-1.8.ebuild
+++ b/sci-biology/BRAKER/BRAKER-1.8.ebuild
@@ -35,6 +35,10 @@ RDEPEND="${DEPEND}
S="${WORKDIR}"/BRAKER_v"${PV}"
+src_prepare(){
+ sed -e 's/^use helpMod/use BRAKER::helpMod/' -i braker.pl || die
+}
+
src_install(){
perl_set_version
dobin *.pl
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/BRAKER/
@ 2016-12-03 18:51 Martin Mokrejs
0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2016-12-03 18:51 UTC (permalink / raw
To: gentoo-commits
commit: c976d64e8e6458c02d70ec3aeb8a883e86c26e37
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Dec 3 18:51:08 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Dec 3 18:51:08 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c976d64e
sci-biology/BRAKER: version bump, point to additional dependency
Package-Manager: portage-2.3.2
sci-biology/BRAKER/{BRAKER-1.8.ebuild => BRAKER-1.9.ebuild} | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/sci-biology/BRAKER/BRAKER-1.8.ebuild b/sci-biology/BRAKER/BRAKER-1.9.ebuild
similarity index 90%
rename from sci-biology/BRAKER/BRAKER-1.8.ebuild
rename to sci-biology/BRAKER/BRAKER-1.9.ebuild
index 439b5c2..4074279 100644
--- a/sci-biology/BRAKER/BRAKER-1.8.ebuild
+++ b/sci-biology/BRAKER/BRAKER-1.9.ebuild
@@ -26,8 +26,7 @@ DEPEND=""
RDEPEND="${DEPEND}
dev-perl/Scalar-Util-Numeric
sci-biology/augustus"
-# Current version of BRAKER1 1.8 requires GeneMark-ET v.4.29 (or up).
-
+ #>=sci-biology/GeneMark_ET-bin-4.29"
#
# BUG:
# this causes:
@@ -48,6 +47,6 @@ src_install(){
}
pkg_postinst(){
- einfo "Please install GeneMark-ET >= v.4.29 after obtaininig a license from"
+ einfo "Please install sci-biology/GeneMark_ET after obtaininig a license and binaries from"
einfo "http://exon.gatech.edu/GeneMark/gmes_instructions.html"
}
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/BRAKER/
@ 2018-01-08 14:11 Martin Mokrejs
0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2018-01-08 14:11 UTC (permalink / raw
To: gentoo-commits
commit: e506aabb717f6536e683c88a998e7b566aab8164
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jan 8 14:11:10 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jan 8 14:11:10 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e506aabb
sci-biology/BRAKER: version bump
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/BRAKER/{BRAKER-1.9.ebuild => BRAKER-2.ebuild} | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/BRAKER/BRAKER-1.9.ebuild b/sci-biology/BRAKER/BRAKER-2.ebuild
similarity index 89%
rename from sci-biology/BRAKER/BRAKER-1.9.ebuild
rename to sci-biology/BRAKER/BRAKER-2.ebuild
index 7c814763f..b4c752457 100644
--- a/sci-biology/BRAKER/BRAKER-1.9.ebuild
+++ b/sci-biology/BRAKER/BRAKER-2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -10,7 +10,7 @@ DESCRIPTION="Gene prediction based on RNA-Seq using GeneMark-ET and AUGUSTUS"
# http://bioinf.uni-greifswald.de/bioinf/publications/pag2015.pdf
HOMEPAGE="http://bioinf.uni-greifswald.de/bioinf/braker
http://bioinf.uni-greifswald.de/augustus/downloads"
-SRC_URI=" http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1_v"${PV}".tar.gz -> ${P}.tar.gz"
+SRC_URI="http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER"${PV}".tar.gz -> ${P}.tar.gz"
# Download BRAKER1 from http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1.tar.gz.
# The most recent release is version 1.8, from December 15th 2015.
# Example data for testing the BRAKER1 pipeline is available at
@@ -31,7 +31,7 @@ RDEPEND="${DEPEND}
# this causes:
# [blocks B ] <perl-core/Scalar-List-Utils-1.380.0 ("<perl-core/Scalar-List-Utils-1.380.0" is blocking virtual/perl-Scalar-List-Utils-1.380.0)
-S="${WORKDIR}"/BRAKER_v"${PV}"
+S="${WORKDIR}"/BRAKER_v"${PV}".0
src_prepare(){
sed -e 's/^use helpMod/use BRAKER::helpMod/' -i braker.pl || die
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/BRAKER/
@ 2018-03-31 0:15 Martin Mokrejs
0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2018-03-31 0:15 UTC (permalink / raw
To: gentoo-commits
commit: 3724acdd4d192ac400d81a94f91e957c0e832ccd
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Mar 31 00:15:01 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Mar 31 00:15:01 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3724acdd
sci-biology/BRAKER: version bump, update LICENSE
Package-Manager: Portage-2.3.24, Repoman-2.3.6
.../{BRAKER-2.ebuild => BRAKER-2.1.0.ebuild} | 30 +++++++++-------------
1 file changed, 12 insertions(+), 18 deletions(-)
diff --git a/sci-biology/BRAKER/BRAKER-2.ebuild b/sci-biology/BRAKER/BRAKER-2.1.0.ebuild
similarity index 58%
rename from sci-biology/BRAKER/BRAKER-2.ebuild
rename to sci-biology/BRAKER/BRAKER-2.1.0.ebuild
index b4c752457..13d63d4b8 100644
--- a/sci-biology/BRAKER/BRAKER-2.ebuild
+++ b/sci-biology/BRAKER/BRAKER-2.1.0.ebuild
@@ -10,15 +10,17 @@ DESCRIPTION="Gene prediction based on RNA-Seq using GeneMark-ET and AUGUSTUS"
# http://bioinf.uni-greifswald.de/bioinf/publications/pag2015.pdf
HOMEPAGE="http://bioinf.uni-greifswald.de/bioinf/braker
http://bioinf.uni-greifswald.de/augustus/downloads"
-SRC_URI="http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER"${PV}".tar.gz -> ${P}.tar.gz"
-# Download BRAKER1 from http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1.tar.gz.
-# The most recent release is version 1.8, from December 15th 2015.
-# Example data for testing the BRAKER1 pipeline is available at
-# http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1examples.tar.gz (1.1 GB).
-
-LICENSE="GPL-3"
+SRC_URI="http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER_v"${PV}".tar.gz -> ${P}.tar.gz"
+# Example data for testing the BRAKER2 pipeline is available at
+# http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER2examples.tar.gz (1.1 GB).
+
+# BRAKER2 is using the Artistic-1.0 version without clause 8 about
+# commercial distribution
+# See discussion at https://opensource.org/licenses/artistic-license-1.0
+# Practically the license is same as http://dev.perl.org/licenses/artistic.html
+LICENSE="Artistic"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64 ~x86"
IUSE=""
DEPEND=""
@@ -26,23 +28,15 @@ RDEPEND="${DEPEND}
dev-perl/Scalar-Util-Numeric
sci-biology/augustus"
#>=sci-biology/GeneMark_ET-bin-4.29"
-#
-# BUG:
-# this causes:
-# [blocks B ] <perl-core/Scalar-List-Utils-1.380.0 ("<perl-core/Scalar-List-Utils-1.380.0" is blocking virtual/perl-Scalar-List-Utils-1.380.0)
-
-S="${WORKDIR}"/BRAKER_v"${PV}".0
-src_prepare(){
- sed -e 's/^use helpMod/use BRAKER::helpMod/' -i braker.pl || die
-}
+S="${WORKDIR}"/BRAKER_v"${PV}"
src_install(){
perl_set_version
dobin *.pl
insinto ${VENDOR_LIB}/${PN}
doins *.pm
- dodoc README.braker
+ dodoc userguide.pdf
}
pkg_postinst(){
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/BRAKER/
@ 2019-07-18 17:12 Martin Mokrejs
0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2019-07-18 17:12 UTC (permalink / raw
To: gentoo-commits
commit: c7a40f0c2955843da5c85d0abbeed58351547ce1
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jul 18 17:12:10 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jul 18 17:12:10 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c7a40f0c
sci-biology/BRAKER: version bump
New HOMEPAGE, SRC_URI, layout of .tar.gz tarball
Package-Manager: Portage-2.3.69, Repoman-2.3.16
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
.../BRAKER/{BRAKER-2.1.0.ebuild => BRAKER-2.1.2.ebuild} | 15 +++++++--------
1 file changed, 7 insertions(+), 8 deletions(-)
diff --git a/sci-biology/BRAKER/BRAKER-2.1.0.ebuild b/sci-biology/BRAKER/BRAKER-2.1.2.ebuild
similarity index 79%
rename from sci-biology/BRAKER/BRAKER-2.1.0.ebuild
rename to sci-biology/BRAKER/BRAKER-2.1.2.ebuild
index 13d63d4b8..908e57e51 100644
--- a/sci-biology/BRAKER/BRAKER-2.1.0.ebuild
+++ b/sci-biology/BRAKER/BRAKER-2.1.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -8,9 +8,10 @@ inherit perl-module
DESCRIPTION="Gene prediction based on RNA-Seq using GeneMark-ET and AUGUSTUS"
# http://bioinf.uni-greifswald.de/bioinf/publications/pag2015.pdf
-HOMEPAGE="http://bioinf.uni-greifswald.de/bioinf/braker
+HOMEPAGE="https://github.com/Gaius-Augustus/BRAKER
+ http://bioinf.uni-greifswald.de/bioinf/braker
http://bioinf.uni-greifswald.de/augustus/downloads"
-SRC_URI="http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER_v"${PV}".tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/Gaius-Augustus/BRAKER/archive/v${PV}.tar.gz -> ${P}.tar.gz"
# Example data for testing the BRAKER2 pipeline is available at
# http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER2examples.tar.gz (1.1 GB).
@@ -29,14 +30,12 @@ RDEPEND="${DEPEND}
sci-biology/augustus"
#>=sci-biology/GeneMark_ET-bin-4.29"
-S="${WORKDIR}"/BRAKER_v"${PV}"
-
src_install(){
perl_set_version
- dobin *.pl
+ dobin scripts/*.pl
insinto ${VENDOR_LIB}/${PN}
- doins *.pm
- dodoc userguide.pdf
+ doins scripts/*.pm
+ dodoc docs/userguide.pdf
}
pkg_postinst(){
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/BRAKER/
@ 2020-12-25 18:35 Horea Christian
0 siblings, 0 replies; 13+ messages in thread
From: Horea Christian @ 2020-12-25 18:35 UTC (permalink / raw
To: gentoo-commits
commit: 0329e0493d40516a501aea07d2d9c95f8c8c2dd3
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Dec 25 18:35:04 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Dec 25 18:35:04 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0329e049
sci-biology/BRAKER: EAPI bump 7
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/BRAKER/BRAKER-2.1.2.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/BRAKER/BRAKER-2.1.2.ebuild b/sci-biology/BRAKER/BRAKER-2.1.2.ebuild
index 908e57e51..448ca2463 100644
--- a/sci-biology/BRAKER/BRAKER-2.1.2.ebuild
+++ b/sci-biology/BRAKER/BRAKER-2.1.2.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
-PERL_EXPORT_PHASE_FUNCTIONS=no
+#PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module
DESCRIPTION="Gene prediction based on RNA-Seq using GeneMark-ET and AUGUSTUS"
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/BRAKER/
@ 2021-03-18 18:54 Andrew Ammerlaan
0 siblings, 0 replies; 13+ messages in thread
From: Andrew Ammerlaan @ 2021-03-18 18:54 UTC (permalink / raw
To: gentoo-commits
commit: acc57b34ce2bf932901a478ccd70a25e25da7dde
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Mar 18 18:37:24 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Mar 18 18:37:24 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=acc57b34
sci-biology/BRAKER: use perl_domodule
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/BRAKER/BRAKER-2.1.2.ebuild | 7 ++-----
1 file changed, 2 insertions(+), 5 deletions(-)
diff --git a/sci-biology/BRAKER/BRAKER-2.1.2.ebuild b/sci-biology/BRAKER/BRAKER-2.1.2.ebuild
index 448ca2463..150bf55a1 100644
--- a/sci-biology/BRAKER/BRAKER-2.1.2.ebuild
+++ b/sci-biology/BRAKER/BRAKER-2.1.2.ebuild
@@ -1,9 +1,8 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-#PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module
DESCRIPTION="Gene prediction based on RNA-Seq using GeneMark-ET and AUGUSTUS"
@@ -22,7 +21,6 @@ SRC_URI="https://github.com/Gaius-Augustus/BRAKER/archive/v${PV}.tar.gz -> ${P}.
LICENSE="Artistic"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
@@ -33,8 +31,7 @@ RDEPEND="${DEPEND}
src_install(){
perl_set_version
dobin scripts/*.pl
- insinto ${VENDOR_LIB}/${PN}
- doins scripts/*.pm
+ perl_domodule scripts/*.pm
dodoc docs/userguide.pdf
}
^ permalink raw reply related [flat|nested] 13+ messages in thread
end of thread, other threads:[~2021-03-18 18:54 UTC | newest]
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