aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorMartin Mokrejs <mmokrejs@fold.natur.cuni.cz>2019-03-07 19:41:26 +0100
committerMartin Mokrejs <mmokrejs@fold.natur.cuni.cz>2019-03-07 19:41:26 +0100
commit3ae295ae35d49fc7242ae20b64611ebccc0daec3 (patch)
treeffa5ff18d1ebda0a6c5eac2636ac154d19aae7c1
parentsci-biology/ParaAT: new package (diff)
downloadsci-3ae295ae35d49fc7242ae20b64611ebccc0daec3.tar.gz
sci-3ae295ae35d49fc7242ae20b64611ebccc0daec3.tar.bz2
sci-3ae295ae35d49fc7242ae20b64611ebccc0daec3.zip
sci-biology/KaKs_Calculator: new package
Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
-rw-r--r--sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild22
-rw-r--r--sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild48
-rw-r--r--sci-biology/KaKs_Calculator/Manifest6
-rw-r--r--sci-biology/KaKs_Calculator/files/KaKs_Calculator-1.2_strlen_was_not_declared.patch11
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>