diff options
| -rw-r--r-- | academic/paml/LICENSE | 3 | ||||
| -rw-r--r-- | academic/paml/paml.SlackBuild | 38 | ||||
| -rw-r--r-- | academic/paml/paml.info | 12 |
3 files changed, 19 insertions, 34 deletions
diff --git a/academic/paml/LICENSE b/academic/paml/LICENSE deleted file mode 100644 index b58e2508621b4..0000000000000 --- 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 1445b81259671..63af805f4e826 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 7c31ba8a044c2..02959b6afddc4 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="" |