commit: 3ae295ae35d49fc7242ae20b64611ebccc0daec3 Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Thu Mar 7 18:41:26 2019 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Thu Mar 7 18:41:26 2019 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3ae295ae
sci-biology/KaKs_Calculator: new package Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz> .../KaKs_Calculator/KaKs_Calculator-1.2.ebuild | 22 +++++++--- .../KaKs_Calculator/KaKs_Calculator-2.0.ebuild | 48 ++++++++++++++++++++++ ...Ks_Calculator-1.2_strlen_was_not_declared.patch | 11 +++++ 3 files changed, 75 insertions(+), 6 deletions(-) diff --git a/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild b/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild index ccd592626..929117604 100644 --- a/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild +++ b/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild @@ -1,24 +1,33 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +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://code.google.com/p/kaks-calculator + http://bigd.big.ac.cn/tools/kaks"; SRC_URI=" - https://kaks-calculator.googlecode.com/files/KaKs_Calculator"${PV}".tar.gz - https://kaks-calculator.googlecode.com/files/parseFastaIntoAXT.pl"; + https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/kaks-calculator/KaKs_Calculator"${PV}".tar.gz -> ${P}.tar.gz + https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/kaks-calculator/parseFastaIntoAXT.pl + https://raw.githubusercontent.com/WilsonSayresLab/AlignmentProcessor/master/KaKs_Calculator/${PN}${PV}/KaKs_CalculatorDOC.pdf -> ${P}_manual.pdf + https://s3.amazonaws.com/fumba.me/share+files/1-s2.0-S1672022907600072-main.pdf -> ${PN}-Zhang_et_al_2006.pdf" LICENSE="GPL-3" SLOT="0" -KEYWORDS="" +KEYWORDS="~amd64 ~x86" IUSE="" +PATCHES=( "${FILESDIR}/${PN}"-1.2_strlen_was_not_declared.patch ) + +# ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments +# http://cbb.big.ac.cn/software +# https://www.sciencedirect.com/science/article/pii/S0006291X12003518 DEPEND="sci-biology/ParaAT" RDEPEND=" dev-lang/perl + sci-biology/paml ${DEPEND}" S="${WORKDIR}"/KaKs_Calculator"${PV}" @@ -36,4 +45,5 @@ src_compile(){ src_install(){ dobin "${DISTDIR}"/parseFastaIntoAXT.pl dobin src/{KaKs_Calculator,AXTConvertor,ConPairs} + dodoc "${DISTDIR}"/${P}_manual.pdf "${DISTDIR}"/${PN}-Zhang_et_al_2006.pdf } diff --git a/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild b/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild new file mode 100644 index 000000000..5edd1323a --- /dev/null +++ b/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit eutils toolchain-funcs + +DESCRIPTION="Calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates" +HOMEPAGE="https://code.google.com/p/kaks-calculator + https://sourceforge.net/projects/kakscalculator2/ + 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://s3.amazonaws.com/fumba.me/share+files/1-s2.0-S1672022907600072-main.pdf -> ${PN}-Zhang_et_al_2006.pdf" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +PATCHES=( "${FILESDIR}/${PN}"-1.2_strlen_was_not_declared.patch ) + +# ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments +# http://cbb.big.ac.cn/software +# https://www.sciencedirect.com/science/article/pii/S0006291X12003518 +DEPEND="sci-biology/ParaAT" +RDEPEND=" + dev-lang/perl + sci-biology/paml + ${DEPEND}" + +S="${WORKDIR}"/KaKs_Calculator"${PV}" + +src_prepare(){ + sed -e "s/^CC = g++/CC="$(tc-getCXX)"/; s/^CFLAGS/#CFLAGS/" -i src/makefile || die + default +} + +src_compile(){ + cd src || die + default +} + +src_install(){ + dobin src/{KaKs_Calculator,AXTConvertor,ConPairs} + dodoc "${DISTDIR}"/${P}_manual.pdf "${DISTDIR}"/${PN}-Zhang_et_al_2006.pdf +} diff --git a/sci-biology/KaKs_Calculator/files/KaKs_Calculator-1.2_strlen_was_not_declared.patch b/sci-biology/KaKs_Calculator/files/KaKs_Calculator-1.2_strlen_was_not_declared.patch new file mode 100644 index 000000000..bb8804f51 --- /dev/null +++ b/sci-biology/KaKs_Calculator/files/KaKs_Calculator-1.2_strlen_was_not_declared.patch @@ -0,0 +1,11 @@ +--- KaKs_Calculator1.2/src/base.h 2006-05-17 14:45:52.000000000 +0200 ++++ KaKs_Calculator1.2/src/base.h 2019-03-07 17:55:08.663688693 +0100 +@@ -39,6 +39,8 @@ + #define max2(a,b) ((a)>(b)?(a):(b)) + #define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a)) + ++#include <string.h> ++ + /* Stanard lib of C++ */ + #include<string> + #include<iostream>
