* [gentoo-commits] proj/sci:master commit in: sci-biology/KaKs_Calculator/
@ 2015-03-21 1:15 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2015-03-21 1:15 UTC (permalink / raw
To: gentoo-commits
commit: 0b7f4bf5b3512c1ee1107bb8d76b962c69e0a1b9
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Mar 21 01:14:26 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Mar 21 01:14:26 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0b7f4bf5
sci-biology/KaKs_Calculator: new package but code does not compile; awaiting some answer from upstream http://cbb.big.ac.cn/Zhang_Zhang
Package-Manager: portage-2.2.15
sci-biology/KaKs_Calculator/ChangeLog | 10 ++++++
.../KaKs_Calculator/KaKs_Calculator-1.2.ebuild | 38 ++++++++++++++++++++++
sci-biology/KaKs_Calculator/metadata.xml | 9 +++++
3 files changed, 57 insertions(+)
diff --git a/sci-biology/KaKs_Calculator/ChangeLog b/sci-biology/KaKs_Calculator/ChangeLog
new file mode 100644
index 0000000..2a3e92f
--- /dev/null
+++ b/sci-biology/KaKs_Calculator/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/KaKs_Calculator
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*KaKs_Calculator-1.2 (21 Mar 2015)
+
+ 21 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +KaKs_Calculator-1.2.ebuild, +metadata.xml:
+ sci-biology/KaKs_Calculator: new package but code does not compile; awaiting
+ some answer from upstream http://cbb.big.ac.cn/Zhang_Zhang
diff --git a/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild b/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
new file mode 100644
index 0000000..5d9bb67
--- /dev/null
+++ b/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates"
+HOMEPAGE="https://code.google.com/p/kaks-calculator"
+SRC_URI="https://kaks-calculator.googlecode.com/files/KaKs_Calculator"${PV}".tar.gz
+ https://kaks-calculator.googlecode.com/files/parseFastaIntoAXT.pl"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sci-biology/ParaAT"
+RDEPEND="
+ dev-lang/perl
+ ${DEPEND}"
+
+S="${WORKDIR}"/KaKs_Calculator"${PV}"
+
+src_prepare(){
+ sed -e "s/^CC = g++/CC="$(tc-getCXX)"/; s/^CFLAGS/#CFLAGS/" -i src/makefile
+}
+
+src_compile(){
+ cd src || die
+ emake
+}
+
+src_install(){
+ dobin "${DISTDIR}"/parseFastaIntoAXT.pl
+ dobin src/{KaKs_Calculator,AXTConvertor,ConPairs}
+}
diff --git a/sci-biology/KaKs_Calculator/metadata.xml b/sci-biology/KaKs_Calculator/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/KaKs_Calculator/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] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/KaKs_Calculator/
@ 2017-02-26 8:48 Justin Lecher
0 siblings, 0 replies; 5+ messages in thread
From: Justin Lecher @ 2017-02-26 8:48 UTC (permalink / raw
To: gentoo-commits
commit: 2a0656b30e719f8a5663509dd728a28ba3940498
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 26 08:46:49 2017 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Feb 26 08:48:51 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2a0656b3
sci-biology/KaKs_Calculator: Bump to EAPI=6
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild | 10 ++++++----
sci-biology/KaKs_Calculator/metadata.xml | 2 +-
2 files changed, 7 insertions(+), 5 deletions(-)
diff --git a/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild b/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
index efd7cb120..ccd592626 100644
--- a/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
+++ b/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
@@ -1,13 +1,14 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=6
inherit eutils toolchain-funcs
DESCRIPTION="Calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates"
HOMEPAGE="https://code.google.com/p/kaks-calculator"
-SRC_URI="https://kaks-calculator.googlecode.com/files/KaKs_Calculator"${PV}".tar.gz
+SRC_URI="
+ https://kaks-calculator.googlecode.com/files/KaKs_Calculator"${PV}".tar.gz
https://kaks-calculator.googlecode.com/files/parseFastaIntoAXT.pl"
LICENSE="GPL-3"
@@ -23,7 +24,8 @@ RDEPEND="
S="${WORKDIR}"/KaKs_Calculator"${PV}"
src_prepare(){
- sed -e "s/^CC = g++/CC="$(tc-getCXX)"/; s/^CFLAGS/#CFLAGS/" -i src/makefile
+ sed -e "s/^CC = g++/CC="$(tc-getCXX)"/; s/^CFLAGS/#CFLAGS/" -i src/makefile || die
+ default
}
src_compile(){
diff --git a/sci-biology/KaKs_Calculator/metadata.xml b/sci-biology/KaKs_Calculator/metadata.xml
index 1699e58b2..f68a1b6fa 100644
--- a/sci-biology/KaKs_Calculator/metadata.xml
+++ b/sci-biology/KaKs_Calculator/metadata.xml
@@ -5,7 +5,7 @@
<email>mmokrejs@fold.natur.cuni.cz</email>
<name>Martin Mokrejs</name>
</maintainer>
-<maintainer type="project">
+ <maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/KaKs_Calculator/
@ 2019-03-29 23:58 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2019-03-29 23:58 UTC (permalink / raw
To: gentoo-commits
commit: 9434b7843e92befab076411b1b39764ff4a35738
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 29 23:58:06 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 29 23:58:06 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9434b784
sci-biology/KaKs_Calculator: fix download URL
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild b/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
index 5edd1323a..e6620b359 100644
--- a/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
+++ b/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
@@ -11,7 +11,7 @@ HOMEPAGE="https://code.google.com/p/kaks-calculator
https://www.sciencedirect.com/science/article/pii/S1672022910600083"
SRC_URI="
https://netcologne.dl.sourceforge.net/project/kakscalculator2/${PN}${PV}.tar.gz -> ${P}.tar.gz
- https://github.com/WilsonSayresLab/AlignmentProcessor/blob/master/KaKs_Calculator/${PN}${PV}/${PN}${PV}_manual.pdf -> ${P}_manual.pdf
+ https://raw.githubusercontent.com/WilsonSayresLab/AlignmentProcessor/master/"{$PN}"/"{$PN}${PV}"/"{$PN}${PV}"_manual.pdf -> ${P}_manual.pdf
https://s3.amazonaws.com/fumba.me/share+files/1-s2.0-S1672022907600072-main.pdf -> ${PN}-Zhang_et_al_2006.pdf"
LICENSE="GPL-3"
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/KaKs_Calculator/
@ 2019-03-30 0:05 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2019-03-30 0:05 UTC (permalink / raw
To: gentoo-commits
commit: 21fc7bb7e17bc4bd4f44f8f80a357f260d3d3748
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Mar 30 00:04:54 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Mar 30 00:04:54 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=21fc7bb7
sci-biology/KaKs_Calculator: another attempt at SRC_URI
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild b/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
index e6620b359..643352424 100644
--- a/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
+++ b/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
@@ -11,7 +11,7 @@ HOMEPAGE="https://code.google.com/p/kaks-calculator
https://www.sciencedirect.com/science/article/pii/S1672022910600083"
SRC_URI="
https://netcologne.dl.sourceforge.net/project/kakscalculator2/${PN}${PV}.tar.gz -> ${P}.tar.gz
- https://raw.githubusercontent.com/WilsonSayresLab/AlignmentProcessor/master/"{$PN}"/"{$PN}${PV}"/"{$PN}${PV}"_manual.pdf -> ${P}_manual.pdf
+ https://raw.githubusercontent.com/WilsonSayresLab/AlignmentProcessor/master/${PN}/${PN}${PV}/${PN}${PV}_manual.pdf -> ${P}_manual.pdf
https://s3.amazonaws.com/fumba.me/share+files/1-s2.0-S1672022907600072-main.pdf -> ${PN}-Zhang_et_al_2006.pdf"
LICENSE="GPL-3"
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/KaKs_Calculator/
@ 2021-01-20 9:06 Andrew Ammerlaan
0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2021-01-20 9:06 UTC (permalink / raw
To: gentoo-commits
commit: e8675df9c13fff7ba985478d6d0bb827b26255dd
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Jan 20 09:00:45 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Jan 20 09:00:45 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e8675df9
sci-biology/KaKs_Calculator: update homepage
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild | 5 ++---
sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild | 4 ++--
2 files changed, 4 insertions(+), 5 deletions(-)
diff --git a/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild b/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
index 929117604..a731be61c 100644
--- a/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
+++ b/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -6,8 +6,7 @@ EAPI=7
inherit eutils toolchain-funcs
DESCRIPTION="Calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates"
-HOMEPAGE="https://code.google.com/p/kaks-calculator
- http://bigd.big.ac.cn/tools/kaks"
+HOMEPAGE="https://bigd.big.ac.cn/tools/kaks"
SRC_URI="
https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/kaks-calculator/KaKs_Calculator"${PV}".tar.gz -> ${P}.tar.gz
https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/kaks-calculator/parseFastaIntoAXT.pl
diff --git a/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild b/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
index 643352424..89b4fe03c 100644
--- a/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
+++ b/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -6,7 +6,7 @@ EAPI=7
inherit eutils toolchain-funcs
DESCRIPTION="Calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates"
-HOMEPAGE="https://code.google.com/p/kaks-calculator
+HOMEPAGE="
https://sourceforge.net/projects/kakscalculator2/
https://www.sciencedirect.com/science/article/pii/S1672022910600083"
SRC_URI="
^ permalink raw reply related [flat|nested] 5+ messages in thread
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