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

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

[Martin Mokrejs]

commit:     b01f66fab12d15b2ab19af9f8ca677924dbd6132
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue May  5 15:11:40 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue May  5 15:11:40 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b01f66fa

sci-biology/polyphen: package skeleton

Package-Manager: portage-2.2.18

 sci-biology/polyphen/ChangeLog             |  9 +++++++++
 sci-biology/polyphen/metadata.xml          |  9 +++++++++
 sci-biology/polyphen/polyphen-2.2.2.ebuild | 27 +++++++++++++++++++++++++++
 3 files changed, 45 insertions(+)

diff --git a/sci-biology/polyphen/ChangeLog b/sci-biology/polyphen/ChangeLog
new file mode 100644
index 0000000..da1810a
--- /dev/null
+++ b/sci-biology/polyphen/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/polyphen
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*polyphen-2.2.2 (05 May 2015)
+
+  05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
+  +polyphen-2.2.2.ebuild:
+  sci-biology/polyphen: package skeleton

diff --git a/sci-biology/polyphen/metadata.xml b/sci-biology/polyphen/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/polyphen/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/polyphen/polyphen-2.2.2.ebuild b/sci-biology/polyphen/polyphen-2.2.2.ebuild
new file mode 100644
index 0000000..3f602cf
--- /dev/null
+++ b/sci-biology/polyphen/polyphen-2.2.2.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Predict effect of aminoacid substitution on human protein function"
+HOMEPAGE="http://genetics.bwh.harvard.edu/pph2/dokuwiki/start"
+SRC_URI="http://genetics.bwh.harvard.edu/pph2/dokuwiki/_media/polyphen-2.2.2r405b.tar.gz"
+
+LICENSE="polyphen" # for non-commercial use only
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+# 3.7GB
+# ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-databases-2011_12.tar.bz2
+
+# 2.4GB
+# ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-mlc-2011_12.tar.bz2
+
+# 895MB
+# ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-multiz-2009_10.tar.bz2
+

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

[Justin Lecher]

commit:     e770a3c197257bcf967b1efa7df16436bfa9ccf1
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 21 16:02:52 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 21 16:02:52 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e770a3c1

sci-biology/polyphen: Drop empty lines

Package-Manager: portage-2.2.20.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/polyphen/polyphen-2.2.2.ebuild | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/sci-biology/polyphen/polyphen-2.2.2.ebuild b/sci-biology/polyphen/polyphen-2.2.2.ebuild
index 5ffb60d..6038eee 100644
--- a/sci-biology/polyphen/polyphen-2.2.2.ebuild
+++ b/sci-biology/polyphen/polyphen-2.2.2.ebuild
@@ -13,9 +13,6 @@ SLOT="0"
 KEYWORDS=""
 IUSE=""
 
-DEPEND=""
-RDEPEND="${DEPEND}"
-
 # 3.7GB
 # ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-databases-2011_12.tar.bz2
 
@@ -24,4 +21,3 @@ RDEPEND="${DEPEND}"
 
 # 895MB
 # ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-multiz-2009_10.tar.bz2
-

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

[Andrew Ammerlaan]

commit:     9c2dcdf491c442611763b878fba0c3240daf1d42
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Feb  3 05:40:53 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Feb  3 05:40:53 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9c2dcdf4

sci-biology/polyphen: EAPI bump, fix configure, compile and install

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

 sci-biology/polyphen/polyphen-2.2.2.ebuild | 38 ++++++++++++++++++++++++++++--
 1 file changed, 36 insertions(+), 2 deletions(-)

diff --git a/sci-biology/polyphen/polyphen-2.2.2.ebuild b/sci-biology/polyphen/polyphen-2.2.2.ebuild
index 0995356fd..da07819a5 100644
--- a/sci-biology/polyphen/polyphen-2.2.2.ebuild
+++ b/sci-biology/polyphen/polyphen-2.2.2.ebuild
@@ -5,11 +5,21 @@ EAPI=7
 
 DESCRIPTION="Predict effect of aminoacid substitution on human protein function"
 HOMEPAGE="http://genetics.bwh.harvard.edu/pph2/dokuwiki/start"
-SRC_URI="http://genetics.bwh.harvard.edu/pph2/dokuwiki/_media/polyphen-${PV}r405d.tar.gz"
+SRC_URI="
+	http://genetics.bwh.harvard.edu/pph2/dokuwiki/_media/polyphen-${PV}r405d.tar.gz
+	http://mafft.cbrc.jp/alignment/software/mafft-7.221-without-extensions-src.tgz
+	http://prdownloads.sourceforge.net/weka/weka-3-6-12.zip
+"
 
 LICENSE="polyphen" # for non-commercial use only
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
+
+DEPEND="
+	dev-perl/CGI
+	sci-biology/ncbi-blast+
+"
+RDEPEND="${DEPEND}"
 
 # 3.7GB
 # ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-databases-2011_12.tar.bz2
@@ -19,3 +29,27 @@ KEYWORDS=""
 
 # 895MB
 # ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-multiz-2009_10.tar.bz2
+
+src_unpack() {
+	unpack "polyphen-${PV}r405d.tar.gz"
+	cp "${DISTDIR}/mafft-7.221-without-extensions-src.tgz" "${S}/src" || die
+	cp "${DISTDIR}/weka-3-6-12.zip" "${S}/src" || die
+}
+
+src_configure() {
+	# non-standard configure script
+	./configure
+}
+
+src_compile() {
+	pushd src
+	emake -j1
+	popd
+}
+
+src_install() {
+	pushd src
+	default
+	popd
+	einstalldocs
+}

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

[Andrew Ammerlaan]

commit:     9242fb651f31c1774aac1fecfd58f64a49d3770c
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Feb  4 10:17:26 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Feb  4 10:17:26 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9242fb65

sci-biology/polyphen: add bdep on unzip

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

 sci-biology/polyphen/polyphen-2.2.2.ebuild | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sci-biology/polyphen/polyphen-2.2.2.ebuild b/sci-biology/polyphen/polyphen-2.2.2.ebuild
index da07819a5..3100c6bbd 100644
--- a/sci-biology/polyphen/polyphen-2.2.2.ebuild
+++ b/sci-biology/polyphen/polyphen-2.2.2.ebuild
@@ -20,6 +20,7 @@ DEPEND="
 	sci-biology/ncbi-blast+
 "
 RDEPEND="${DEPEND}"
+BDEPEND="app-arch/unzip"
 
 # 3.7GB
 # ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-databases-2011_12.tar.bz2

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

[Andrew Ammerlaan]

commit:     98b76dd9389c5dfe59897373d568033c1999ab1e
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May  2 12:27:05 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May  2 12:27:05 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=98b76dd9

sci-biology/polyphen: treeclean

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/polyphen/metadata.xml          | 12 -------
 sci-biology/polyphen/polyphen-2.2.2.ebuild | 56 ------------------------------
 2 files changed, 68 deletions(-)

diff --git a/sci-biology/polyphen/metadata.xml b/sci-biology/polyphen/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/polyphen/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?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>

diff --git a/sci-biology/polyphen/polyphen-2.2.2.ebuild b/sci-biology/polyphen/polyphen-2.2.2.ebuild
deleted file mode 100644
index 3100c6bbd..000000000
--- a/sci-biology/polyphen/polyphen-2.2.2.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Predict effect of aminoacid substitution on human protein function"
-HOMEPAGE="http://genetics.bwh.harvard.edu/pph2/dokuwiki/start"
-SRC_URI="
-	http://genetics.bwh.harvard.edu/pph2/dokuwiki/_media/polyphen-${PV}r405d.tar.gz
-	http://mafft.cbrc.jp/alignment/software/mafft-7.221-without-extensions-src.tgz
-	http://prdownloads.sourceforge.net/weka/weka-3-6-12.zip
-"
-
-LICENSE="polyphen" # for non-commercial use only
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND="
-	dev-perl/CGI
-	sci-biology/ncbi-blast+
-"
-RDEPEND="${DEPEND}"
-BDEPEND="app-arch/unzip"
-
-# 3.7GB
-# ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-databases-2011_12.tar.bz2
-
-# 2.4GB
-# ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-mlc-2011_12.tar.bz2
-
-# 895MB
-# ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-multiz-2009_10.tar.bz2
-
-src_unpack() {
-	unpack "polyphen-${PV}r405d.tar.gz"
-	cp "${DISTDIR}/mafft-7.221-without-extensions-src.tgz" "${S}/src" || die
-	cp "${DISTDIR}/weka-3-6-12.zip" "${S}/src" || die
-}
-
-src_configure() {
-	# non-standard configure script
-	./configure
-}
-
-src_compile() {
-	pushd src
-	emake -j1
-	popd
-}
-
-src_install() {
-	pushd src
-	default
-	popd
-	einstalldocs
-}