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authorMartin Mokrejs <mmokrejs@fold.natur.cuni.cz>2019-03-07 20:43:41 +0100
committerMartin Mokrejs <mmokrejs@fold.natur.cuni.cz>2019-03-07 20:43:41 +0100
commite75a3d6b5e82f3ca53ef356f21afe0369e82eac1 (patch)
tree04d203c3b3733306539e5ad0f394661b3ad67a02
parentsci-biology/CAT: new package (diff)
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sci-biology/CAT: add missing -lstdc++ -lm and drop -w
Use proper env variables 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.ebuild9
-rw-r--r--sci-biology/CAT/files/CAT-1.3_respect_env_variables.patch15
2 files changed, 16 insertions, 8 deletions
diff --git a/sci-biology/CAT/CAT-1.3.ebuild b/sci-biology/CAT/CAT-1.3.ebuild
index 2628c04a9..44d099524 100644
--- a/sci-biology/CAT/CAT-1.3.ebuild
+++ b/sci-biology/CAT/CAT-1.3.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-DESCRIPTION="Estimate codon usage bias and its statistical significance"
+DESCRIPTION="Codon usage bias (composition) and its statistical significance"
HOMEPAGE="
http://bigd.big.ac.cn/tools/cat
http://cbb.big.ac.cn/Software
@@ -11,9 +11,9 @@ HOMEPAGE="
http://www.cbrc.kaust.edu.sa/CAT"
SRC_URI="ftp://download.big.ac.cn/bigd/tools/${PN}${PV}.tar.gz -> ${P}.tar.gz"
-LICENSE="GPL-3"
+LICENSE="GPL-3+"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64 ~x86"
IUSE=""
PATCHES=( "${FILESDIR}"/CAT-1.3_respect_env_variables.patch )
@@ -30,5 +30,8 @@ src_compile(){
}
src_install(){
+ dodoc README.TXT
+ newdoc doc/CAT-DOC.pdf "${PN}".pdf
+ cd src || die
dobin CAT
}
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
index 5dff3986c..9c32d8a1d 100644
--- a/sci-biology/CAT/files/CAT-1.3_respect_env_variables.patch
+++ b/sci-biology/CAT/files/CAT-1.3_respect_env_variables.patch
@@ -1,11 +1,16 @@
---- 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 @@
+--- CAT1.3/src/makefile.ori 2011-03-13 15:05:27.000000000 +0100
++++ CAT1.3/src/makefile 2019-03-07 20:31:27.147985682 +0100
+@@ -1,10 +1,10 @@
PRGS = CAT
-CC = g++
-CFLAGS = -O3
-+CC ?= g++
-+CFLAGS ?= -O3
++CXX ?= g++
++CXXFLAGS ?= -O3
all: $(PRGS)
+ CAT: main_CAT.cpp CAT.cpp base.cpp
+- $(CC) $(CFLAGS) -o $@ main_CAT.cpp CAT.cpp base.cpp -w
++ $(CXX) $(CXXFLAGS) -o $@ main_CAT.cpp CAT.cpp base.cpp -lstdc++ -lm
+ install: CAT
+ install CAT ~/bin/