From 078f15de57d3a1c3b6a15201878d837cca32b70f Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Sat, 14 Dec 2013 08:52:33 +0700 Subject: academic/pamlX: Added (A GUI for PAML). Signed-off-by: Willy Sudiarto Raharjo --- academic/pamlX/README | 1 + academic/pamlX/doinst.sh | 3 ++ academic/pamlX/pamlX.SlackBuild | 116 ++++++++++++++++++++++++++++++++++++++++ academic/pamlX/pamlX.desktop | 9 ++++ academic/pamlX/pamlX.info | 10 ++++ academic/pamlX/slack-desc | 19 +++++++ 6 files changed, 158 insertions(+) create mode 100644 academic/pamlX/README create mode 100644 academic/pamlX/doinst.sh create mode 100644 academic/pamlX/pamlX.SlackBuild create mode 100644 academic/pamlX/pamlX.desktop create mode 100644 academic/pamlX/pamlX.info create mode 100644 academic/pamlX/slack-desc (limited to 'academic') diff --git a/academic/pamlX/README b/academic/pamlX/README new file mode 100644 index 0000000000..d2ab78a000 --- /dev/null +++ b/academic/pamlX/README @@ -0,0 +1 @@ +The graphical user interface for paml. diff --git a/academic/pamlX/doinst.sh b/academic/pamlX/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/pamlX/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi diff --git a/academic/pamlX/pamlX.SlackBuild b/academic/pamlX/pamlX.SlackBuild new file mode 100644 index 0000000000..86624eb5a2 --- /dev/null +++ b/academic/pamlX/pamlX.SlackBuild @@ -0,0 +1,116 @@ +#!/bin/sh + +# Slackware build script for pamlX + +# Copyright 2013 Petar Petrov, petar.petrov@student.oulu.fi +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +PRGNAM=pamlX +VERSION=${VERSION:-1.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i486 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i486" ]; then + SLKCFLAGS="-O2 -march=i486 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION-src +tar xvf $CWD/$PRGNAM-$VERSION-src.tgz +cd $PRGNAM-$VERSION-src +chown -R root:root . +find . \ + \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ + -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ + -exec chmod 644 {} \; + +# Fix the path where pamlX looks for the paml executables, its config +# file (if necessary it should be in your home directory) and the +# manuals installed by paml. +sed -i 's|QApplication::applicationDirPath()|"/usr"|g' mainwindow.cpp +sed -i 's|+= "/pamlx.conf"|= "~/.pamlX/pamlx.conf"|g' mainwindow.cpp +sed -i 's|/doc/|/doc/paml-4.7a/|g' mainwindow.cpp +sed -i 's|/doc/|/doc/paml-4.7a/|g' pamlhistorydialog.cpp + +# If you want the "Help" menu to use something else than Okular for +# viewing the PDF documentation, uncomment the appropriate line below +# (or add your own if you want a viewer not listed here): +# +# sed -i 's|okular|xpdf|g' mainwindow.cpp # Use XPDF +# sed -i 's|okular|evince|g' mainwindow.cpp # Use Evince +# sed -i 's|okular|acroread|g' mainwindow.cpp # Use Adobe Acrobat Reader +# sed -i 's|okular|epdfviewer|g' mainwindow.cpp # Use ePDFViewer + +qmake \ +QMAKE_CFLAGS="$SLKCFLAGS" \ +QMAKE_CXXFLAGS="$SLKCFLAGS" +make + +install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM + +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 $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications +cp pamlxlogo.png $PKG/usr/share/pixmaps/$PRGNAM.png + +# Fix permissions of the documentation control files and examples +find $PKG/usr/{doc,share} -type d -exec chmod 755 {} \; -o \ + -type f -exec chmod 644 {} \; + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/pamlX/pamlX.desktop b/academic/pamlX/pamlX.desktop new file mode 100644 index 0000000000..3d6a0b10c8 --- /dev/null +++ b/academic/pamlX/pamlX.desktop @@ -0,0 +1,9 @@ +[Desktop Entry] +Categories=Education; +Comment=A GUI for PAML +Exec=pamlX +Icon=pamlX +Name=pamlX +StartupNotify=false +Type=Application +GenericName= diff --git a/academic/pamlX/pamlX.info b/academic/pamlX/pamlX.info new file mode 100644 index 0000000000..2a849e49da --- /dev/null +++ b/academic/pamlX/pamlX.info @@ -0,0 +1,10 @@ +PRGNAM="pamlX" +VERSION="1.1" +HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/" +DOWNLOAD="http://abacus.gene.ucl.ac.uk/software/pamlX-1.1-src.tgz" +MD5SUM="8f7472fd5a83e0bf6abf495dc6bcb253" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="paml" +MAINTAINER="Petar Petrov" +EMAIL="petar.petrov@student.oulu.fi" diff --git a/academic/pamlX/slack-desc b/academic/pamlX/slack-desc new file mode 100644 index 0000000000..d1778d8ad3 --- /dev/null +++ b/academic/pamlX/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +pamlX: pamlX (A GUI for PAML) +pamlX: +pamlX: A graphical user interface for PAML +pamlX: +pamlX: Home: http://abacus.gene.ucl.ac.uk/software/paml.html +pamlX: +pamlX: +pamlX: +pamlX: +pamlX: +pamlX: -- cgit v1.2.3