academic/paml: Updated for version 4.10.5.

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

3 files changed, 19 insertions, 34 deletions

diff --git a/academic/paml/LICENSE b/academic/paml/LICENSE
deleted file mode 100644
index b58e250862..0000000000
--- a/academic/paml/LICENSE
+++ /dev/null
@@ -1,3 +0,0 @@
-PAML is maintained and distributed for academic use free of charge by
-Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac
-OSX, and executables are provided for MS Windows.
diff --git a/academic/paml/paml.SlackBuild b/academic/paml/paml.SlackBuild
index 1445b81259..63af805f4e 100644
--- a/academic/paml/paml.SlackBuild
+++ b/academic/paml/paml.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for paml
 
-# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com
+# Copyright 2013-2022 Petar Petrov slackalaxy@gmail.com
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -25,7 +25,7 @@
 cd $(dirname $0) ; CWD=$(pwd)
 
 PRGNAM=paml
-VERSION=${VERSION:-4.9j}
+VERSION=${VERSION:-4.10.5}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 PKGTYPE=${PKGTYPE:-tgz}
@@ -69,9 +69,9 @@ set -e
 rm -rf $PKG
 mkdir -p $TMP $PKG $OUTPUT
 cd $TMP
-rm -rf ${PRGNAM}${VERSION}
-tar xvf $CWD/${PRGNAM}${VERSION}.tgz
-cd ${PRGNAM}${VERSION}
+rm -rf ${PRGNAM}-${VERSION}
+tar xvf $CWD/${PRGNAM}-${VERSION}.tar.gz
+cd ${PRGNAM}-${VERSION}
 chown -R root:root .
 find -L . \
  \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
@@ -112,9 +112,6 @@ install -D -m755 evolverNSsites 	$PKG/usr/libexec/$PRGNAM/evolverNSsites
 # cc $SLKCFLAGS -o TreeTimeJeff TreeTimeJeff.c tools.c -lm
 # install -D -m755 TreeTimeJeff 	$PKG/usr/libexec/$PRGNAM/TreeTimeJeff
 
-# Rename the local README, so we include it in the package.
-mv README.txt README-compiling.txt
-
 # Compile and install NEB, BEB and BranchSite
 cd ../Technical/Simulation/Codon
 cc $SLKCFLAGS -DNEB        -o PositiveSitesNEB PositiveSites.c -lm
@@ -125,38 +122,29 @@ install -D -m755 PositiveSitesBEB 	$PKG/usr/libexec/$PRGNAM/PositiveSitesBEB
 install -D -m755 PositiveSitesBS 	$PKG/usr/libexec/$PRGNAM/PositiveSitesBS
 install -D -m755 PositiveSitesNEB 	$PKG/usr/libexec/$PRGNAM/PositiveSitesNEB
 
-# Rename this README too so we include it in the package.
-mv README.txt README-codon.txt
-
 # Compile and install Multiruns
 cd ..
 cc -o multiruns $SLKCFLAGS multiruns.c -lm
 install -D -m755 multiruns 	$PKG/usr/libexec/$PRGNAM/multiruns
 
-cd $TMP/${PRGNAM}${VERSION}
+cd $TMP/${PRGNAM}-${VERSION}
 
 # Include sample system files and example experimental data.
-mkdir -p $PKG/usr/share/$PRGNAM/{aa,codon,ctl,dat,nuc,paup,trees}
-cp -a *.dat dat/* $PKG/usr/share/$PRGNAM/dat
-cp -a Technical/Simulation/Codon/{codeml.ctl,*.dat} \
-  $PKG/usr/share/$PRGNAM/codon
+mkdir -p $PKG/usr/share/$PRGNAM/Simulation/Codon
+cp -a src/*.ctl dat $PKG/usr/share/$PRGNAM
+cp -a Technical/Simulation/Codon/{codeml.ctl,*.dat,README.txt} \
+  $PKG/usr/share/$PRGNAM/Simulation/Codon
 cp -a examples 	$PKG/usr/share/$PRGNAM
-cp -a *.aa 	$PKG/usr/share/$PRGNAM/aa
-cp -a *.ctl 	$PKG/usr/share/$PRGNAM/ctl
-cp -a *.nuc 	$PKG/usr/share/$PRGNAM/nuc
-cp -a paup* 	$PKG/usr/share/$PRGNAM/paup
-cp -a *.trees 	$PKG/usr/share/$PRGNAM/trees
 
 find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
   | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
 
 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
-cp -a README.txt GeneticCode.txt doc/* src/README-compiling.txt \
-  Technical/{Pt/eigenQREV.pdf,Simulation/{multiruns.txt,Codon/README-codon.txt}}\
+cp -a README.md LICENSE doc/* \
   $PKG/usr/doc/$PRGNAM-$VERSION
-cat $CWD/MCMCtree.Tutorials.pdf > $PKG/usr/doc/$PRGNAM-$VERSION/MCMCtree.Tutorial.pdf
+cp Technical/Pt/eigenQREV.pdf $PKG/usr/doc/$PRGNAM-$VERSION
+cp $CWD/MCMCtreeDOC.pdf $PKG/usr/doc/$PRGNAM-$VERSION
 cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
-cat $CWD/LICENSE > $PKG/usr/doc/$PRGNAM-$VERSION/LICENSE
 
 # Fix permissions.
 find $PKG/usr/{doc,share} -type d -exec chmod 755 {} \; -o \
diff --git a/academic/paml/paml.info b/academic/paml/paml.info
index 7c31ba8a04..02959b6afd 100644
--- a/academic/paml/paml.info
+++ b/academic/paml/paml.info
@@ -1,10 +1,10 @@
 PRGNAM="paml"
-VERSION="4.9j"
-HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html"
-DOWNLOAD="http://abacus.gene.ucl.ac.uk/software/paml4.9j.tgz \
-          http://ponce.cc/slackware/sources/repo/MCMCtree.Tutorials.pdf"
-MD5SUM="50c1760512b7a5df50305e5fd26d0ca5 \
-        29c851d887eea56b949c01ab42cc48fb"
+VERSION="4.10.5"
+HOMEPAGE="https://github.com/abacus-gene/paml/"
+DOWNLOAD="https://github.com/abacus-gene/paml/archive/v4.10.5/paml-4.10.5.tar.gz \
+	https://raw.githubusercontent.com/slackalaxy/sources/main/MCMCtreeDOC.pdf"
+MD5SUM="9247980ad975757595ec1bf98464af76 \
+	99de7c0241b7152d619d899d72775410"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES=""