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

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

[Martin Mokrejs]

commit:     354715b5a7fdb31d7737e9f8d53e804b32237770
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Feb 10 15:27:24 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Feb 10 15:27:24 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=354715b5

sci-biology/portrait: new package

Package-Manager: portage-2.2.26

 sci-biology/portrait/metadata.xml        |  9 +++++++++
 sci-biology/portrait/portrait-1.1.ebuild | 30 ++++++++++++++++++++++++++++++
 2 files changed, 39 insertions(+)

diff --git a/sci-biology/portrait/metadata.xml b/sci-biology/portrait/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/portrait/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>

diff --git a/sci-biology/portrait/portrait-1.1.ebuild b/sci-biology/portrait/portrait-1.1.ebuild
new file mode 100644
index 0000000..f75f7b9
--- /dev/null
+++ b/sci-biology/portrait/portrait-1.1.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Ab initio ncRNA prediction"
+HOMEPAGE="http://bioinformatics.cenargen.embrapa.br/portrait"
+SRC_URI="http://bioinformatics.cenargen.embrapa.br/portrait/download/portrait.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="
+	${DEPEND}
+	dev-lang/perl
+	sci-biology/ANGLE-bin
+	sci-biology/cast-bin
+	sci-libs/libsvm"
+# was only tested with sci-libs/libsvm-2.84
+
+src_install(){
+	dobin *.pl
+	dodoc README.txt
+	insinto /usr/share/"${PN}"
+	doins *.model
+}

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

[Martin Mokrejs]

commit:     2a0a97bc233e628ec1994a8b9cc81e3f7b6b9a5f
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Feb 10 16:54:40 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Feb 10 16:54:40 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2a0a97bc

sci-biology/portrait: some minimal code cleanup

Package-Manager: portage-2.2.26

 sci-biology/portrait/portrait-1.1.ebuild | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/sci-biology/portrait/portrait-1.1.ebuild b/sci-biology/portrait/portrait-1.1.ebuild
index f75f7b9..fe8f670 100644
--- a/sci-biology/portrait/portrait-1.1.ebuild
+++ b/sci-biology/portrait/portrait-1.1.ebuild
@@ -23,6 +23,8 @@ RDEPEND="
 # was only tested with sci-libs/libsvm-2.84
 
 src_install(){
+	sed -e 's/\r//' -i *.pl || die "Failed to convert from DOS line endings to Unix"
+	sed -e 's#/home/rtarrial/prog#/usr/bin#' -i *.pl
 	dobin *.pl
 	dodoc README.txt
 	insinto /usr/share/"${PN}"

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

[Martin Mokrejs]

commit:     2e1c2e4408aae4d87589293af913dfa588b679d3
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jul 16 21:53:39 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jul 16 21:53:39 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2e1c2e44

sci-biology/portrait: Rewrite sed hackery (aka DOS2Unix)

Thanks to @mgorny for the hint.
Reported-by: <mgorny <AT> gentoo.org>
Closes: https://bugs.gentoo.org/689816
Package-Manager: Portage-2.3.69, Repoman-2.3.16
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>

 sci-biology/portrait/portrait-1.1.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/portrait/portrait-1.1.ebuild b/sci-biology/portrait/portrait-1.1.ebuild
index 424ccfcd6..d6e0c7e82 100644
--- a/sci-biology/portrait/portrait-1.1.ebuild
+++ b/sci-biology/portrait/portrait-1.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -22,7 +22,7 @@ RDEPEND="
 # was only tested with sci-libs/libsvm-2.84
 
 src_install(){
-	sed -e 's/\r//' -i *.pl || die "Failed to convert from DOS line endings to Unix"
+	sed -e 's/\r//' -i *.pl || die "Failed to convert from DOS line endings to Unix"
 	sed -e 's#/home/rtarrial/prog#/usr/bin#' -i *.pl
 	dobin *.pl
 	dodoc README.txt

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

[Andrew Ammerlaan]

commit:     c5bce1836a079d9b405ef7a5785ddc496ed1dfda
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 16:28:33 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 16:28:33 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c5bce183

sci-biology/portrait: properly name tarball

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

 sci-biology/portrait/portrait-1.1.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/portrait/portrait-1.1.ebuild b/sci-biology/portrait/portrait-1.1.ebuild
index d6e0c7e82..e8da5e51e 100644
--- a/sci-biology/portrait/portrait-1.1.ebuild
+++ b/sci-biology/portrait/portrait-1.1.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
 
 DESCRIPTION="Ab initio ncRNA prediction"
 HOMEPAGE="http://bioinformatics.cenargen.embrapa.br/portrait"
-SRC_URI="http://bioinformatics.cenargen.embrapa.br/portrait/download/portrait.tar.gz"
+SRC_URI="http://bioinformatics.cenargen.embrapa.br/portrait/download/portrait.tar.gz -> ${P}.tar.gz"
 
 LICENSE="GPL-3+"
 SLOT="0"

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

[Andrew Ammerlaan]

commit:     a03b4cb61d86b4d5d11fcad889c1c430e7bdef05
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Feb  3 05:45:12 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Feb  3 05:45:12 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a03b4cb6

sci-biology/portrait: EAPI bump

Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/portrait/portrait-1.1.ebuild | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/sci-biology/portrait/portrait-1.1.ebuild b/sci-biology/portrait/portrait-1.1.ebuild
index e8da5e51e..81da03922 100644
--- a/sci-biology/portrait/portrait-1.1.ebuild
+++ b/sci-biology/portrait/portrait-1.1.ebuild
@@ -1,7 +1,7 @@
 # Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="Ab initio ncRNA prediction"
 HOMEPAGE="http://bioinformatics.cenargen.embrapa.br/portrait"
@@ -9,8 +9,7 @@ SRC_URI="http://bioinformatics.cenargen.embrapa.br/portrait/download/portrait.ta
 
 LICENSE="GPL-3+"
 SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
 
 DEPEND=""
 RDEPEND="