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

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

[Martin Mokrejs]

commit:     3f78358286d681fd4f41ce8a366a45988d70f8b1
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Feb 10 15:23:58 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Feb 10 15:23:58 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3f783582

sci-biology/ANGLE-bin: new package

Package-Manager: portage-2.2.26

 sci-biology/ANGLE-bin/ANGLE-bin-20080813.ebuild | 33 +++++++++++++++++++++++++
 sci-biology/ANGLE-bin/metadata.xml              | 12 +++++++++
 2 files changed, 45 insertions(+)

diff --git a/sci-biology/ANGLE-bin/ANGLE-bin-20080813.ebuild b/sci-biology/ANGLE-bin/ANGLE-bin-20080813.ebuild
new file mode 100644
index 0000000..44bc582
--- /dev/null
+++ b/sci-biology/ANGLE-bin/ANGLE-bin-20080813.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="CDS prediction overcoming sequencing errors in protein coding regions in unfinished cDNA"
+HOMEPAGE="http://bioinformatics.cenargen.embrapa.br/portrait/download"
+SRC_URI="http://bioinformatics.cenargen.embrapa.br/portrait/download/angle.tar.gz"
+
+RESTRICT="fetch"
+# According to Roberto T Arrial (author of portrait) for the purpose of his
+# portrait project the binaries were provided under a BSD license.
+# The output from Angle is modified for use with portrait and differs from
+# current versions at http://cbrc3.cbrc.jp/~shimizu/index.php
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/angle
+
+src_install(){
+	dobin *.pl ANGLE-linux64 ANGLE-linux32 ANGLE-linux32DP ANGLE-linux64DP
+	dodoc README.txt
+	insinto /usr/share/"${PN}"
+	doins test.html sample.txt sample2.txt "test" seq2.noOrf
+	doins -r param-human
+	doins -r param-plant
+}

diff --git a/sci-biology/ANGLE-bin/metadata.xml b/sci-biology/ANGLE-bin/metadata.xml
new file mode 100644
index 0000000..1699e58
--- /dev/null
+++ b/sci-biology/ANGLE-bin/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>

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

[Justin Lecher]

commit:     ba3dccfe4b84b6ae9691313434c8a5407b872b16
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 26 09:41:50 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Feb 26 09:41:50 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ba3dccfe

sci-biology/ANGLE-bin: Properly support amd64/x86

* Chop DESCRIPTION to < 80 chars
* Bump to EAPI=6
* Create versioned source tarball
* Silence QA warnings for prebuilt binaries

Package-Manager: portage-2.2.27
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 ...0080813.ebuild => ANGLE-bin-20080813-r1.ebuild} | 24 +++++++++++-----------
 sci-biology/ANGLE-bin/metadata.xml                 |  2 +-
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/sci-biology/ANGLE-bin/ANGLE-bin-20080813.ebuild b/sci-biology/ANGLE-bin/ANGLE-bin-20080813-r1.ebuild
similarity index 63%
rename from sci-biology/ANGLE-bin/ANGLE-bin-20080813.ebuild
rename to sci-biology/ANGLE-bin/ANGLE-bin-20080813-r1.ebuild
index 4cbc822..55dc837 100644
--- a/sci-biology/ANGLE-bin/ANGLE-bin-20080813.ebuild
+++ b/sci-biology/ANGLE-bin/ANGLE-bin-20080813-r1.ebuild
@@ -2,32 +2,32 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
 
-DESCRIPTION="CDS prediction overcoming sequencing errors in protein coding regions in unfinished cDNA"
+DESCRIPTION="CDS prediction overcoming sequencing errors in unfinished cDNA"
 HOMEPAGE="http://bioinformatics.cenargen.embrapa.br/portrait/download"
-SRC_URI="http://bioinformatics.cenargen.embrapa.br/portrait/download/angle.tar.gz"
+SRC_URI="http://bioinformatics.cenargen.embrapa.br/portrait/download/angle.tar.gz -> ${P}.tar.gz"
 
-RESTRICT="fetch"
 # According to Roberto T Arrial (author of portrait) for the purpose of his
 # portrait project the binaries were provided under a BSD license.
 # The output from Angle is modified for use with portrait and differs from
 # current versions at http://cbrc3.cbrc.jp/~shimizu/index.php
 LICENSE="BSD"
 SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-DEPEND=""
-RDEPEND="${DEPEND}"
-
 S="${WORKDIR}"/angle
 
+QA_PREBUILT="opt/*"
+
 src_install(){
-	dobin *.pl ANGLE-linux64 ANGLE-linux32 ANGLE-linux32DP ANGLE-linux64DP
+	into /opt
+	dobin *.pl
+	use amd64 && dobin ANGLE-linux64 ANGLE-linux64DP
+	use x86 && dobin ANGLE-linux32 ANGLE-linux32DP
 	dodoc README.txt
 	insinto /usr/share/"${PN}"
-	doins test.html sample.txt sample2.txt "test" seq2.noOrf
-	doins -r param-human
-	doins -r param-plant
+	doins test.html sample.txt sample2.txt test seq2.noOrf
+	doins -r param-human param-plant
 }

diff --git a/sci-biology/ANGLE-bin/metadata.xml b/sci-biology/ANGLE-bin/metadata.xml
index 1699e58..f68a1b6 100644
--- a/sci-biology/ANGLE-bin/metadata.xml
+++ b/sci-biology/ANGLE-bin/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>

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

[Andrew Ammerlaan]

commit:     b90f110a9b54ade2bb63f453390f1ae5bf0e1f6c
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Fri Mar  5 15:17:26 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Fri Mar  5 15:29:11 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b90f110a

sci-biology/ANGLE-bin: EAPI bump, add missing deps

Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/ANGLE-bin/ANGLE-bin-20080813-r1.ebuild | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/sci-biology/ANGLE-bin/ANGLE-bin-20080813-r1.ebuild b/sci-biology/ANGLE-bin/ANGLE-bin-20080813-r1.ebuild
index 5716596e3..f6453cd6a 100644
--- a/sci-biology/ANGLE-bin/ANGLE-bin-20080813-r1.ebuild
+++ b/sci-biology/ANGLE-bin/ANGLE-bin-20080813-r1.ebuild
@@ -1,7 +1,9 @@
-# Copyright 1999-2016 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="CDS prediction overcoming sequencing errors in unfinished cDNA"
 HOMEPAGE="http://bioinformatics.cenargen.embrapa.br/portrait/download"
@@ -14,15 +16,18 @@ SRC_URI="http://bioinformatics.cenargen.embrapa.br/portrait/download/angle.tar.g
 LICENSE="BSD"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
-S="${WORKDIR}"/angle
+S="${WORKDIR}/angle"
+
+RDEPEND="
+	sys-libs/libstdc++-v3
+	dev-lang/perl
+"
 
 QA_PREBUILT="opt/*"
 
 src_install(){
-	into /opt
-	dobin *.pl
+	perl_domodule *.pl
 	use amd64 && dobin ANGLE-linux64 ANGLE-linux64DP
 	use x86 && dobin ANGLE-linux32 ANGLE-linux32DP
 	dodoc README.txt