[gentoo-commits] proj/sci:master commit in: sci-biology/CAT/files/, sci-biology/CAT/

[gentoo-commits] proj/sci:master commit in: sci-biology/CAT/files/, sci-biology/CAT/

[Martin Mokrejs]

commit:     e75a3d6b5e82f3ca53ef356f21afe0369e82eac1
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar  7 19:43:41 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar  7 19:43:41 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e75a3d6b

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 <AT> fold.natur.cuni.cz>

 sci-biology/CAT/CAT-1.3.ebuild                            |  9 ++++++---
 sci-biology/CAT/files/CAT-1.3_respect_env_variables.patch | 15 ++++++++++-----
 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/