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authorMartin Mokrejs <mmokrejs@fold.natur.cuni.cz>2019-03-07 20:20:38 +0100
committerMartin Mokrejs <mmokrejs@fold.natur.cuni.cz>2019-03-07 20:20:38 +0100
commit2b35fa3317ef51f0de6002b65efa23605ee5e0cb (patch)
tree2920b513c8d9c4aeab3a9928e717757c7ceeac28
parentsci-biology/ParaAT: add missing default in src_prepare() (diff)
downloadsci-2b35fa3317ef51f0de6002b65efa23605ee5e0cb.tar.gz
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sci-biology/CAT: new package
Does not compile, probably requires some older C++ standard? 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/CAT/CAT-1.3.ebuild34
-rw-r--r--sci-biology/CAT/Manifest1
-rw-r--r--sci-biology/CAT/files/CAT-1.3_respect_env_variables.patch11
-rw-r--r--sci-biology/CAT/metadata.xml12
4 files changed, 58 insertions, 0 deletions
diff --git a/sci-biology/CAT/CAT-1.3.ebuild b/sci-biology/CAT/CAT-1.3.ebuild
new file mode 100644
index 000000000..2628c04a9
--- /dev/null
+++ b/sci-biology/CAT/CAT-1.3.ebuild
@@ -0,0 +1,34 @@
+# Copyright 2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Estimate codon usage bias and its statistical significance"
+HOMEPAGE="
+ http://bigd.big.ac.cn/tools/cat
+ http://cbb.big.ac.cn/Software
+ http://code.google.com/p/composition-analysis-toolkit
+ http://www.cbrc.kaust.edu.sa/CAT"
+SRC_URI="ftp://download.big.ac.cn/bigd/tools/${PN}${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+PATCHES=( "${FILESDIR}"/CAT-1.3_respect_env_variables.patch )
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+BDEPEND=""
+
+S="${WORKDIR}/${PN}${PV}"
+
+src_compile(){
+ cd src || die
+ emake
+}
+
+src_install(){
+ dobin CAT
+}
diff --git a/sci-biology/CAT/Manifest b/sci-biology/CAT/Manifest
new file mode 100644
index 000000000..6a092cc28
--- /dev/null
+++ b/sci-biology/CAT/Manifest
@@ -0,0 +1 @@
+DIST CAT-1.3.tar.gz 1377451 BLAKE2B 835da7949d5158d324314cbd586c7492143dff19eb13e204995f9eb04fa748604e31bfc1c34b7ead73d81548544ec22089575caaa3ecd2f79ef64a6d06802475 SHA512 4ea060efe58dd4a4d4146d5b5f2651b2cef5ae34ac83ec98eff9618d39930c3c05bf1f6949c38c0a2461a82d9fc53361e5f72108071787b4263acb20e4f56e8c
diff --git a/sci-biology/CAT/files/CAT-1.3_respect_env_variables.patch b/sci-biology/CAT/files/CAT-1.3_respect_env_variables.patch
new file mode 100644
index 000000000..5dff3986c
--- /dev/null
+++ b/sci-biology/CAT/files/CAT-1.3_respect_env_variables.patch
@@ -0,0 +1,11 @@
+--- CAT1.3/src/makefile 2011-03-13 15:05:27.000000000 +0100
++++ CAT1.3/src/makefile 2019-03-07 20:08:29.988220775 +0100
+@@ -1,6 +1,6 @@
+ PRGS = CAT
+-CC = g++
+-CFLAGS = -O3
++CC ?= g++
++CFLAGS ?= -O3
+
+ all: $(PRGS)
+
diff --git a/sci-biology/CAT/metadata.xml b/sci-biology/CAT/metadata.xml
new file mode 100644
index 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/CAT/metadata.xml
@@ -0,0 +1,12 @@
+<?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>