[gentoo-commits] proj/sci:master commit in: sci-biology/GAL/, sci-biology/GAL/files/

2022-01-25 Thread Andrew Ammerlaan 
commit: 19eb71e9e2cc023a547e9ca34c246d0266dcbcf2
Author: Andrew Ammerlaan  gentoo  org>
AuthorDate: Tue Jan 25 09:55:06 2022 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Tue Jan 25 09:55:06 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=19eb71e9

sci-biology/GAL: fix install

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan  gentoo.org>

 sci-biology/GAL/GAL-0.2.2_p20200508.ebuild | 19 ---
 sci-biology/GAL/files/Build.PL.patch   | 24 +---
 2 files changed, 21 insertions(+), 22 deletions(-)

diff --git a/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild 
b/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild
index 1aa7e99be..f02907368 100644
--- a/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild
+++ b/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 inherit perl-module
 
@@ -10,16 +10,15 @@ COMMIT="94af39622aab5ba48eb693f2327f6e90f1d202ed"
 DESCRIPTION="Genome Annotation Library (incl. fasta_tool)"
 HOMEPAGE="https://github.com/The-Sequence-Ontology/GAL;
 SRC_URI="https://github.com/The-Sequence-Ontology/GAL/archive/${COMMIT}.tar.gz 
-> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-${COMMIT}"
 
 LICENSE="( GPL-1+ Artistic )"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
 
 RESTRICT="test"
 
 DEPEND="
-   >=dev-lang/perl-5.6.1
-   dev-perl/Module-Build
dev-perl/Config-Std
virtual/perl-Data-Dumper
dev-perl/Data-Types
@@ -29,6 +28,7 @@ DEPEND="
dev-perl/Number-Format
virtual/perl-Scalar-List-Utils
dev-perl/Set-IntSpan-Fast
+   dev-perl/Statistics-Descriptive
dev-perl/Statistics-Descriptive-Discrete
dev-perl/Template-Toolkit
dev-perl/Text-Graph
@@ -36,7 +36,12 @@ DEPEND="
dev-perl/Text-Table
dev-perl/Exception-Class
dev-perl/Test-Warn
-   dev-perl/URI"
+   dev-perl/URI
+   sci-biology/fasta
+"
 RDEPEND="${DEPEND}"
+BDEPEND="dev-perl/Module-Build"
 
-S="${WORKDIR}/${PN}-${COMMIT}"
+PATCHES=(
+   "${FILESDIR}/Build.PL.patch"
+)

diff --git a/sci-biology/GAL/files/Build.PL.patch 
b/sci-biology/GAL/files/Build.PL.patch
index 6d881f249..eee4fb60d 100644
--- a/sci-biology/GAL/files/Build.PL.patch
+++ b/sci-biology/GAL/files/Build.PL.patch
@@ -1,16 +1,11 @@
-diff -ruN GAL_0.2.2.orig/Build.PL GAL_0.2.2/Build.PL
 GAL_0.2.2.orig/Build.PL2014-01-30 01:35:11.0 +0100
-+++ GAL_0.2.2/Build.PL 2016-01-02 12:09:16.212623256 +0100
-@@ -6,26 +6,6 @@
- my $class = Module::Build->subclass
-   (
-class => 'Module::Build::Custom',
--   code => q{
--   sub ACTION_build {
--   my $self = shift;
--   $self->SUPER::ACTION_build;
--   $self->dispatch('installdeps');
--   }
+diff --git a/Build.PL b/Build.PL
+index 5915ca8..61eceb3 100644
+--- a/Build.PL
 b/Build.PL
+@@ -12,19 +12,6 @@ my $class = Module::Build->subclass
+$self->SUPER::ACTION_build;
+$self->dispatch('installdeps');
+}
 -   sub ACTION_install {
 - my $self = shift;
 - print "\n\nGAL does not do a system wide install\n\n";
@@ -24,7 +19,6 @@ diff -ruN GAL_0.2.2.orig/Build.PL GAL_0.2.2/Build.PL
 - print "remove the entire subroutine (ACTION_install) where this 
message\n";
 - print "is printed run Build realclean and re-install.\n\n";
 -   }
-- },
+  },
);
  
- my $builder = $class->new(

[gentoo-commits] proj/sci:master commit in: sci-biology/GAL/

2021-01-19 Thread Andrew Ammerlaan 
commit: 421630ddde61a0a4c49e4a3f53830022d1494e2a
Author: Andrew Ammerlaan  riseup  net>
AuthorDate: Tue Jan 19 13:54:41 2021 +
Commit: Andrew Ammerlaan  riseup  net>
CommitDate: Tue Jan 19 13:54:41 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=421630dd

sci-biology/GAL: EAPI bump, fix fetching

Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan  riseup.net>

 sci-biology/GAL/GAL-0.2.2_p20200508.ebuild | 13 +
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild 
b/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild
index 445b9eaa3..1aa7e99be 100644
--- a/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild
+++ b/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -13,7 +13,9 @@ 
SRC_URI="https://github.com/The-Sequence-Ontology/GAL/archive/${COMMIT}.tar.gz -
 
 LICENSE="( GPL-1+ Artistic )"
 SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
+
+RESTRICT="test"
 
 DEPEND="
>=dev-lang/perl-5.6.1
@@ -37,9 +39,4 @@ DEPEND="
dev-perl/URI"
 RDEPEND="${DEPEND}"
 
-S="${WORKDIR}/${PN}_${PV}"
-
-src_prepare(){
-   default
-   epatch "${FILESDIR}"/Build.PL.patch
-}
+S="${WORKDIR}/${PN}-${COMMIT}"

[gentoo-commits] proj/sci:master commit in: sci-biology/GAL/

2017-01-31 Thread Martin Mokrejs 
commit: 1b87ed6e019e93e97d474b1bab5bfdb08c25937b
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Tue Jan 31 12:44:42 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Jan 31 12:44:42 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1b87ed6e

sci-biology/GAL: added additional deps

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/GAL/GAL-0.2.2.ebuild | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/sci-biology/GAL/GAL-0.2.2.ebuild b/sci-biology/GAL/GAL-0.2.2.ebuild
index 6a01474..ace781f 100644
--- a/sci-biology/GAL/GAL-0.2.2.ebuild
+++ b/sci-biology/GAL/GAL-0.2.2.ebuild
@@ -18,13 +18,15 @@ IUSE=""
 DEPEND="
>=dev-lang/perl-5.6.1
dev-perl/Module-Build
+   dev-perl/Config-Std
virtual/perl-Data-Dumper
+   dev-perl/Data-Types
dev-perl/DBD-SQLite
dev-perl/DBIx-Class
dev-perl/IO-All
dev-perl/Number-Format
virtual/perl-Scalar-List-Utils
-   dev-perl/Set-IntSpan
+   dev-perl/Set-IntSpan-Fast
dev-perl/Statistics-Descriptive-Discrete
dev-perl/Template-Toolkit
dev-perl/Text-Graph

[gentoo-commits] proj/sci:master commit in: sci-biology/GAL/

2017-01-31 Thread Martin Mokrejs 
commit: 98edbec85e3f24bacaf5a56688a85f391e05a8aa
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Tue Jan 31 10:59:35 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Jan 31 10:59:35 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=98edbec8

sci-biology/GAL: depend on virtuals

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/GAL/GAL-0.2.2.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/GAL/GAL-0.2.2.ebuild b/sci-biology/GAL/GAL-0.2.2.ebuild
index 86a3eeb..6a01474 100644
--- a/sci-biology/GAL/GAL-0.2.2.ebuild
+++ b/sci-biology/GAL/GAL-0.2.2.ebuild
@@ -18,12 +18,12 @@ IUSE=""
 DEPEND="
>=dev-lang/perl-5.6.1
dev-perl/Module-Build
-   perl-core/Data-Dumper
+   virtual/perl-Data-Dumper
dev-perl/DBD-SQLite
dev-perl/DBIx-Class
dev-perl/IO-All
dev-perl/Number-Format
-   perl-core/Scalar-List-Utils
+   virtual/perl-Scalar-List-Utils
dev-perl/Set-IntSpan
dev-perl/Statistics-Descriptive-Discrete
dev-perl/Template-Toolkit

[gentoo-commits] proj/sci:master commit in: sci-biology/GAL/

2017-01-31 Thread Martin Mokrejs 
commit: d82b7f0131d896a1d27ec77f97167b292015c5ce
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Tue Jan 31 10:58:06 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Jan 31 10:58:06 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d82b7f01

sci-biology/GAL: add more dependencies

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/GAL/GAL-0.2.2.ebuild | 6 --
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/sci-biology/GAL/GAL-0.2.2.ebuild b/sci-biology/GAL/GAL-0.2.2.ebuild
index 7117253..86a3eeb 100644
--- a/sci-biology/GAL/GAL-0.2.2.ebuild
+++ b/sci-biology/GAL/GAL-0.2.2.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
 # $Id$
 
@@ -18,9 +18,12 @@ IUSE=""
 DEPEND="
>=dev-lang/perl-5.6.1
dev-perl/Module-Build
+   perl-core/Data-Dumper
+   dev-perl/DBD-SQLite
dev-perl/DBIx-Class
dev-perl/IO-All
dev-perl/Number-Format
+   perl-core/Scalar-List-Utils
dev-perl/Set-IntSpan
dev-perl/Statistics-Descriptive-Discrete
dev-perl/Template-Toolkit
@@ -29,7 +32,6 @@ DEPEND="
dev-perl/Text-Table
dev-perl/Exception-Class
dev-perl/Test-Warn
-   dev-perl/DBIx-Class
dev-perl/URI"
 RDEPEND="${DEPEND}"

[gentoo-commits] proj/sci:master commit in: sci-biology/GAL/

2016-01-04 Thread Martin Mokrejs 
commit: 9d11e87f14c8d9aefad761fe871794538d41d3e2
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Mon Jan  4 14:53:17 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Jan  4 14:53:17 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9d11e87f

sci-biology/GAL: fix some package names in DEPEND to match actual CPAN packages

Package-Manager: portage-2.2.26

 sci-biology/GAL/ChangeLog| 4 
 sci-biology/GAL/GAL-0.2.2.ebuild | 4 ++--
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/sci-biology/GAL/ChangeLog b/sci-biology/GAL/ChangeLog
index 7ad355f..3cfe9d4 100644
--- a/sci-biology/GAL/ChangeLog
+++ b/sci-biology/GAL/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  04 Jan 2016; Martin Mokrejs  GAL-0.2.2.ebuild:
+  sci-biology/GAL: fix some package names in DEPEND to match actual CPAN
+  packages
+
   02 Jan 2016; Andreas K. Huettel  files/Build.PL.patch:
   Force systemwide installation by removing all the manual build fiddling
 

diff --git a/sci-biology/GAL/GAL-0.2.2.ebuild b/sci-biology/GAL/GAL-0.2.2.ebuild
index 8275477..c81f6df 100644
--- a/sci-biology/GAL/GAL-0.2.2.ebuild
+++ b/sci-biology/GAL/GAL-0.2.2.ebuild
@@ -23,13 +23,13 @@ DEPEND="
dev-perl/Number-Format
dev-perl/Set-IntSpan
dev-perl/Statistics-Descriptive-Discrete
-   dev-perl/Template
+   dev-perl/Template-Toolkit
dev-perl/Text-Graph
dev-perl/Text-RecordParser
dev-perl/Text-Table
dev-perl/Exception-Class
dev-perl/Test-Warn
-   dev-perl/DBIx-Class-ResultClass-HashRefInflator
+   dev-perl/DBIx-Class
dev-perl/URI"
 RDEPEND="${DEPEND}"

[gentoo-commits] proj/sci:master commit in: sci-biology/GAL/

2016-01-02 Thread Martin Mokrejs 
commit: 0c571eaf1b1b778709d9aacbfb7c81bc4fd0f4a8
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Sat Jan  2 10:06:23 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sat Jan  2 10:06:23 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0c571eaf

sci-biology/GAL: add another perl DEPENDency

Package-Manager: portage-2.2.26

 sci-biology/GAL/ChangeLog| 5 -
 sci-biology/GAL/GAL-0.2.2.ebuild | 5 +++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/sci-biology/GAL/ChangeLog b/sci-biology/GAL/ChangeLog
index 838a7b5..d65ee90 100644
--- a/sci-biology/GAL/ChangeLog
+++ b/sci-biology/GAL/ChangeLog
@@ -1,7 +1,10 @@
 # ChangeLog for sci-biology/GAL
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  02 Jan 2016; Martin Mokrejs  GAL-0.2.2.ebuild:
+  sci-biology/GAL: add another perl DEPENDency
+
 *GAL-0.2.1 (31 Dec 2015)
 *GAL-0.2.2 (31 Dec 2015)
 

diff --git a/sci-biology/GAL/GAL-0.2.2.ebuild b/sci-biology/GAL/GAL-0.2.2.ebuild
index 3b70e1c..8275477 100644
--- a/sci-biology/GAL/GAL-0.2.2.ebuild
+++ b/sci-biology/GAL/GAL-0.2.2.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
 # $Header: $
 
@@ -29,7 +29,8 @@ DEPEND="
dev-perl/Text-Table
dev-perl/Exception-Class
dev-perl/Test-Warn
-   dev-perl/DBIx-Class-ResultClass-HashRefInflator"
+   dev-perl/DBIx-Class-ResultClass-HashRefInflator
+   dev-perl/URI"
 RDEPEND="${DEPEND}"
 
 S="${WORKDIR}/${PN}_${PV}"

[gentoo-commits] proj/sci:master commit in: sci-biology/GAL/, sci-biology/GAL/files/

2016-01-02 Thread Andreas Hüttel 
commit: 6948b58df6416c3938ccbb7fb2657cc515cc7c50
Author: Andreas K. Hüttel  gentoo  org>
AuthorDate: Sat Jan  2 11:11:28 2016 +
Commit: Andreas Hüttel  gentoo  org>
CommitDate: Sat Jan  2 11:11:28 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6948b58d

Force systemwide installation by removing all the manual build fiddling

Package-Manager: portage-2.2.26

 sci-biology/GAL/ChangeLog|  3 +++
 sci-biology/GAL/files/Build.PL.patch | 38 +++-
 2 files changed, 32 insertions(+), 9 deletions(-)

diff --git a/sci-biology/GAL/ChangeLog b/sci-biology/GAL/ChangeLog
index d65ee90..7ad355f 100644
--- a/sci-biology/GAL/ChangeLog
+++ b/sci-biology/GAL/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  02 Jan 2016; Andreas K. Huettel  files/Build.PL.patch:
+  Force systemwide installation by removing all the manual build fiddling
+
   02 Jan 2016; Martin Mokrejs  GAL-0.2.2.ebuild:
   sci-biology/GAL: add another perl DEPENDency
 

diff --git a/sci-biology/GAL/files/Build.PL.patch 
b/sci-biology/GAL/files/Build.PL.patch
index 31b6c73..6d881f2 100644
--- a/sci-biology/GAL/files/Build.PL.patch
+++ b/sci-biology/GAL/files/Build.PL.patch
@@ -1,10 +1,30 @@
 GAL_0.2.2/Build.PL.ori 2016-01-01 00:46:26.0 +0100
-+++ GAL_0.2.2/Build.PL 2016-01-01 00:50:21.0 +0100
-@@ -10,7 +10,6 @@
-sub ACTION_build {
-my $self = shift;
-$self->SUPER::ACTION_build;
+diff -ruN GAL_0.2.2.orig/Build.PL GAL_0.2.2/Build.PL
+--- GAL_0.2.2.orig/Build.PL2014-01-30 01:35:11.0 +0100
 GAL_0.2.2/Build.PL 2016-01-02 12:09:16.212623256 +0100
+@@ -6,26 +6,6 @@
+ my $class = Module::Build->subclass
+   (
+class => 'Module::Build::Custom',
+-   code => q{
+-   sub ACTION_build {
+-   my $self = shift;
+-   $self->SUPER::ACTION_build;
 -   $self->dispatch('installdeps');
-}
-sub ACTION_install {
-  my $self = shift;
+-   }
+-   sub ACTION_install {
+- my $self = shift;
+- print "\n\nGAL does not do a system wide install\n\n";
+- print "To make the libraries and scripts accessible\n";
+- print "modify the paths to fit your system and run the 
following:\n\n";
+- print "export PERL5LIB=\$PERL5LIB:/path/to/GAL/lib\n";
+- print "export PATH=\$PATH:/path/to/GAL/bin\n\n";
+- print "Add those lines to ~/.bash_profile or /etc/profile to\n";
+- print "make those changes permanent.\n\n";
+- print "If you want a system wide install, edit the Build.PL script 
and\n";
+- print "remove the entire subroutine (ACTION_install) where this 
message\n";
+- print "is printed run Build realclean and re-install.\n\n";
+-   }
+- },
+   );
+ 
+ my $builder = $class->new(

[gentoo-commits] proj/sci:master commit in: sci-biology/GAL/

2016-01-01 Thread Martin Mokrejs 
commit: 7bb2e600a2e941545429f393b1ef59ff07260f55
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Fri Jan  1 21:03:34 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Jan  1 21:03:34 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=7bb2e600

sci-biology/GAL: add more perl dependencies; drop old

Package-Manager: portage-2.2.26

 sci-biology/GAL/GAL-0.2.1.ebuild | 25 -
 sci-biology/GAL/GAL-0.2.2.ebuild | 16 +++-
 2 files changed, 15 insertions(+), 26 deletions(-)

diff --git a/sci-biology/GAL/GAL-0.2.1.ebuild b/sci-biology/GAL/GAL-0.2.1.ebuild
deleted file mode 100644
index e84b595..000
--- a/sci-biology/GAL/GAL-0.2.1.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-inherit eutils perl-module
-
-DESCRIPTION="Genome Annotation Library (incl. fasta_tool)"
-HOMEPAGE="http://www.sequenceontology.org/software/GAL.html;
-SRC_URI="http://www.sequenceontology.org/software/GAL_Code/${PN}_${PV}.tar.gz;
-
-LICENSE="( GPL-1+ Artistic )"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="dev-perl/Module-Build"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${PN}_${PV}"
-
-src_prepare(){
-   epatch "${FILESDIR}"/Build.PL.patch
-}

diff --git a/sci-biology/GAL/GAL-0.2.2.ebuild b/sci-biology/GAL/GAL-0.2.2.ebuild
index e84b595..3b70e1c 100644
--- a/sci-biology/GAL/GAL-0.2.2.ebuild
+++ b/sci-biology/GAL/GAL-0.2.2.ebuild
@@ -15,7 +15,21 @@ SLOT="0"
 KEYWORDS=""
 IUSE=""
 
-DEPEND="dev-perl/Module-Build"
+DEPEND="
+   >=dev-lang/perl-5.6.1
+   dev-perl/Module-Build
+   dev-perl/DBIx-Class
+   dev-perl/IO-All
+   dev-perl/Number-Format
+   dev-perl/Set-IntSpan
+   dev-perl/Statistics-Descriptive-Discrete
+   dev-perl/Template
+   dev-perl/Text-Graph
+   dev-perl/Text-RecordParser
+   dev-perl/Text-Table
+   dev-perl/Exception-Class
+   dev-perl/Test-Warn
+   dev-perl/DBIx-Class-ResultClass-HashRefInflator"
 RDEPEND="${DEPEND}"
 
 S="${WORKDIR}/${PN}_${PV}"

[gentoo-commits] proj/sci:master commit in: sci-biology/GAL/

2015-12-31 Thread Martin Mokrejs 
commit: 142e470312ba201d86f14394277f778df3d7afef
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Thu Dec 31 22:23:14 2015 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Dec 31 22:23:14 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=142e4703

sci-biology/GAL: TAP::Harness is provided by dev-lang/perl itself, drop the 
extra DEPENDency

Package-Manager: portage-2.2.26

 sci-biology/GAL/GAL-0.2.1.ebuild | 4 +---
 sci-biology/GAL/GAL-0.2.2.ebuild | 4 +---
 2 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/sci-biology/GAL/GAL-0.2.1.ebuild b/sci-biology/GAL/GAL-0.2.1.ebuild
index 6cfadb1..e8f302c 100644
--- a/sci-biology/GAL/GAL-0.2.1.ebuild
+++ b/sci-biology/GAL/GAL-0.2.1.ebuild
@@ -15,7 +15,5 @@ SLOT="0"
 KEYWORDS=""
 IUSE=""
 
-DEPEND="
-   dev-perl/TAP-Harness
-   dev-perl/Module-Build"
+DEPEND="dev-perl/Module-Build"
 RDEPEND="${DEPEND}"

diff --git a/sci-biology/GAL/GAL-0.2.2.ebuild b/sci-biology/GAL/GAL-0.2.2.ebuild
index 6cfadb1..e8f302c 100644
--- a/sci-biology/GAL/GAL-0.2.2.ebuild
+++ b/sci-biology/GAL/GAL-0.2.2.ebuild
@@ -15,7 +15,5 @@ SLOT="0"
 KEYWORDS=""
 IUSE=""
 
-DEPEND="
-   dev-perl/TAP-Harness
-   dev-perl/Module-Build"
+DEPEND="dev-perl/Module-Build"
 RDEPEND="${DEPEND}"

[gentoo-commits] proj/sci:master commit in: sci-biology/GAL/, sci-biology/GAL/files/

2015-12-31 Thread Martin Mokrejs 
commit: 6867a64802e4652b4c284dc45799ac07abdc22ab
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Thu Dec 31 23:55:45 2015 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Dec 31 23:55:45 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6867a648

sci-biology/GAL: disable automated install of dependencies via CPAN

Package-Manager: portage-2.2.26

 sci-biology/GAL/ChangeLog|  6 --
 sci-biology/GAL/GAL-0.2.1.ebuild |  4 
 sci-biology/GAL/GAL-0.2.2.ebuild |  4 
 sci-biology/GAL/files/Build.PL.patch | 10 ++
 4 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/sci-biology/GAL/ChangeLog b/sci-biology/GAL/ChangeLog
index 8f82b90..838a7b5 100644
--- a/sci-biology/GAL/ChangeLog
+++ b/sci-biology/GAL/ChangeLog
@@ -2,12 +2,6 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
-  31 Dec 2015; Martin Mokrejs  GAL-0.2.1.ebuild,
-  GAL-0.2.2.ebuild:
-  sci-biology/GAL: fix S variable; beware the package is a bundle of many 3rd-
-  party perl modules and apps, it runs wget to fetch additional ones, can't go
-  into the tree as it is now (resolving it now with upstream)
-
 *GAL-0.2.1 (31 Dec 2015)
 *GAL-0.2.2 (31 Dec 2015)
 

diff --git a/sci-biology/GAL/GAL-0.2.1.ebuild b/sci-biology/GAL/GAL-0.2.1.ebuild
index 3bfb6bc..e84b595 100644
--- a/sci-biology/GAL/GAL-0.2.1.ebuild
+++ b/sci-biology/GAL/GAL-0.2.1.ebuild
@@ -19,3 +19,7 @@ DEPEND="dev-perl/Module-Build"
 RDEPEND="${DEPEND}"
 
 S="${WORKDIR}/${PN}_${PV}"
+
+src_prepare(){
+   epatch "${FILESDIR}"/Build.PL.patch
+}

diff --git a/sci-biology/GAL/GAL-0.2.2.ebuild b/sci-biology/GAL/GAL-0.2.2.ebuild
index 3bfb6bc..e84b595 100644
--- a/sci-biology/GAL/GAL-0.2.2.ebuild
+++ b/sci-biology/GAL/GAL-0.2.2.ebuild
@@ -19,3 +19,7 @@ DEPEND="dev-perl/Module-Build"
 RDEPEND="${DEPEND}"
 
 S="${WORKDIR}/${PN}_${PV}"
+
+src_prepare(){
+   epatch "${FILESDIR}"/Build.PL.patch
+}

diff --git a/sci-biology/GAL/files/Build.PL.patch 
b/sci-biology/GAL/files/Build.PL.patch
new file mode 100644
index 000..31b6c73
--- /dev/null
+++ b/sci-biology/GAL/files/Build.PL.patch
@@ -0,0 +1,10 @@
+--- GAL_0.2.2/Build.PL.ori 2016-01-01 00:46:26.0 +0100
 GAL_0.2.2/Build.PL 2016-01-01 00:50:21.0 +0100
+@@ -10,7 +10,6 @@
+sub ACTION_build {
+my $self = shift;
+$self->SUPER::ACTION_build;
+-   $self->dispatch('installdeps');
+}
+sub ACTION_install {
+  my $self = shift;

[gentoo-commits] proj/sci:master commit in: sci-biology/GAL/

2015-12-31 Thread Martin Mokrejs 
commit: 3b9147f553cfb4269f170b001477870d458af241
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Thu Dec 31 21:16:52 2015 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Dec 31 21:16:52 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3b9147f5

sci-biology/GAL: new package, needed by trinityrnaseq and maker

Package-Manager: portage-2.2.26

 sci-biology/GAL/ChangeLog| 10 ++
 sci-biology/GAL/GAL-0.2.1.ebuild | 21 +
 sci-biology/GAL/GAL-0.2.2.ebuild | 21 +
 sci-biology/GAL/metadata.xml |  9 +
 4 files changed, 61 insertions(+)

diff --git a/sci-biology/GAL/ChangeLog b/sci-biology/GAL/ChangeLog
new file mode 100644
index 000..838a7b5
--- /dev/null
+++ b/sci-biology/GAL/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/GAL
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Id$
+
+*GAL-0.2.1 (31 Dec 2015)
+*GAL-0.2.2 (31 Dec 2015)
+
+  31 Dec 2015; Martin Mokrejs  +GAL-0.2.1.ebuild,
+  +GAL-0.2.2.ebuild, +metadata.xml:
+  sci-biology/GAL: new package, needed by trinityrnaseq and maker

diff --git a/sci-biology/GAL/GAL-0.2.1.ebuild b/sci-biology/GAL/GAL-0.2.1.ebuild
new file mode 100644
index 000..6cfadb1
--- /dev/null
+++ b/sci-biology/GAL/GAL-0.2.1.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils perl-module
+
+DESCRIPTION="Genome Annotation Library (incl. fasta_tool)"
+HOMEPAGE="http://www.sequenceontology.org/software/GAL.html;
+SRC_URI="http://www.sequenceontology.org/software/GAL_Code/${PN}_${PV}.tar.gz;
+
+LICENSE="( GPL-1+ Artistic )"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+   dev-perl/TAP-Harness
+   dev-perl/Module-Build"
+RDEPEND="${DEPEND}"

diff --git a/sci-biology/GAL/GAL-0.2.2.ebuild b/sci-biology/GAL/GAL-0.2.2.ebuild
new file mode 100644
index 000..6cfadb1
--- /dev/null
+++ b/sci-biology/GAL/GAL-0.2.2.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils perl-module
+
+DESCRIPTION="Genome Annotation Library (incl. fasta_tool)"
+HOMEPAGE="http://www.sequenceontology.org/software/GAL.html;
+SRC_URI="http://www.sequenceontology.org/software/GAL_Code/${PN}_${PV}.tar.gz;
+
+LICENSE="( GPL-1+ Artistic )"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+   dev-perl/TAP-Harness
+   dev-perl/Module-Build"
+RDEPEND="${DEPEND}"

diff --git a/sci-biology/GAL/metadata.xml b/sci-biology/GAL/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/GAL/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+  sci-biology
+  
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+  
+

[gentoo-commits] proj/sci:master commit in: sci-biology/GAL/

2015-12-31 Thread Martin Mokrejs 
commit: 4d570aec3942c847d10ffc940b43ce55e92ac28e
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Thu Dec 31 23:27:19 2015 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Dec 31 23:27:19 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4d570aec

sci-biology/GAL: fix S variable; beware the package is a bundle of many 
3rd-party perl modules and apps, it runs wget to fetch additional ones, can't 
go into the tree as it is now (resolving it now with upstream)

Package-Manager: portage-2.2.26

 sci-biology/GAL/ChangeLog| 6 ++
 sci-biology/GAL/GAL-0.2.1.ebuild | 2 ++
 sci-biology/GAL/GAL-0.2.2.ebuild | 2 ++
 3 files changed, 10 insertions(+)

diff --git a/sci-biology/GAL/ChangeLog b/sci-biology/GAL/ChangeLog
index 838a7b5..8f82b90 100644
--- a/sci-biology/GAL/ChangeLog
+++ b/sci-biology/GAL/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  31 Dec 2015; Martin Mokrejs  GAL-0.2.1.ebuild,
+  GAL-0.2.2.ebuild:
+  sci-biology/GAL: fix S variable; beware the package is a bundle of many 3rd-
+  party perl modules and apps, it runs wget to fetch additional ones, can't go
+  into the tree as it is now (resolving it now with upstream)
+
 *GAL-0.2.1 (31 Dec 2015)
 *GAL-0.2.2 (31 Dec 2015)
 

diff --git a/sci-biology/GAL/GAL-0.2.1.ebuild b/sci-biology/GAL/GAL-0.2.1.ebuild
index e8f302c..3bfb6bc 100644
--- a/sci-biology/GAL/GAL-0.2.1.ebuild
+++ b/sci-biology/GAL/GAL-0.2.1.ebuild
@@ -17,3 +17,5 @@ IUSE=""
 
 DEPEND="dev-perl/Module-Build"
 RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${PN}_${PV}"

diff --git a/sci-biology/GAL/GAL-0.2.2.ebuild b/sci-biology/GAL/GAL-0.2.2.ebuild
index e8f302c..3bfb6bc 100644
--- a/sci-biology/GAL/GAL-0.2.2.ebuild
+++ b/sci-biology/GAL/GAL-0.2.2.ebuild
@@ -17,3 +17,5 @@ IUSE=""
 
 DEPEND="dev-perl/Module-Build"
 RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${PN}_${PV}"