diff options
4 files changed, 80 insertions, 7 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/Manifest b/sci-biology/KaKs_Calculator/Manifest index c39605893..9e3f8a37d 100644 --- a/sci-biology/KaKs_Calculator/Manifest +++ b/sci-biology/KaKs_Calculator/Manifest @@ -1,2 +1,6 @@ -DIST KaKs_Calculator1.2.tar.gz 2301729 BLAKE2B d8d7812d61b26bce8868e9de59511c0d119c43f725d1f5b4bfbf2b7cddd3c3844e348c9003126ddaff4b0d3d0a0ada2ce1733cda0b1129b7b801114eaaf74f86 SHA512 a1a18229d89262425f879695a1f44ebecbe473c32bcf7ee0d2a2d5d36d34a45b88f5fdcedbacdf0070eb5f0feedff9d74616849aff3cf44f210fdbc65ed56e2c +DIST KaKs_Calculator-1.2.tar.gz 2301729 BLAKE2B d8d7812d61b26bce8868e9de59511c0d119c43f725d1f5b4bfbf2b7cddd3c3844e348c9003126ddaff4b0d3d0a0ada2ce1733cda0b1129b7b801114eaaf74f86 SHA512 a1a18229d89262425f879695a1f44ebecbe473c32bcf7ee0d2a2d5d36d34a45b88f5fdcedbacdf0070eb5f0feedff9d74616849aff3cf44f210fdbc65ed56e2c +DIST KaKs_Calculator-1.2_manual.pdf 72922 BLAKE2B 7c0db9bbca331ecec0e088938217c33c9a70b61732355568a99426663328b2071501c0abf9268d36661ad04af6ea1bf10cb35f72fba03956dc455ff36217e942 SHA512 11c99c4421449ae22d80bf35b063214e3b39d2fa1bd7e7de7a2cfa89aeb0f309f5d1e1cb2fe7cb646c0277d36a951dce04fca00fb957bb713e072d82c9c67566 +DIST KaKs_Calculator-2.0.tar.gz 2104721 BLAKE2B 1782f7ae96695b4a1c01a9f317412bf5e1b910bafbd6f911f97a40eaf459eb2b3b1b65728a7478dff30c00db337f1f4dbae741de569019d2d063688b4f7438d9 SHA512 db8edbd22624a2adb17b3adebc392b1ac327ce0404d6fb184dc9dd8fa3d3b670408b8dc993a29625121610db07ad92bba7613e80abe372ad14bd63248aeda587 +DIST KaKs_Calculator-2.0_manual.pdf 55736 BLAKE2B b8f5103cf7032106e9783fbbddd6417ab1989c090ec770fc474432853d9ca62881c71752a94ea9a0bbbb4442a191ff30b0980d08f78e139f25f99fa471537263 SHA512 ac66a5ec665081778162fc557c609765ae13f30513b3d7cc80d3d400d2f44fbbb54329e2460f7da0c6d8e3fdd26b77c0e86737a0fe721636c34f3ab433dee401 +DIST KaKs_Calculator-Zhang_et_al_2006.pdf 160940 BLAKE2B 2f7e74f44be783f7d7c9973f5d481e54f989733392dee9143a3dc439817d359c3da369d91865c48b4d82ef04d2001cb0ea6d0cea14e1a3a36043ee53b6ac3df1 SHA512 e9a15a41ec4919d302c38f65654beed9cb5a71d9a25f49458dca8a7431a015fa4b955855b97185c2a1d1d19a8fc1f2b0af78f5ab38db3dffec9f14adaa47697a DIST parseFastaIntoAXT.pl 1483 BLAKE2B 5fb82e508bd277cdf1df1b3df63e3449c9569d3334db8f1a259ef69fe45981b40265290c92ba6120b2463809830641878e2cb207118b7dbfc163fad9869e62d9 SHA512 38d39d0fe1f788cf45d742e9fd6b0918a78973faecdb10d98d39384670abdef7212dbd2cdea777f0d5fcbbf202f5331f9fe178ef0f48fafe9e0a31625ab532a1 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> |