From 9639f2f744dad84cea8fe57bf7cc4e0b64ffb03c Mon Sep 17 00:00:00 2001 From: Pedro Mendes Date: Wed, 21 Dec 2011 23:50:15 -0600 Subject: academic/copasi: Added (modeling/simulation of biochemical networks) Signed-off-by: Robby Workman --- academic/copasi/README | 16 ++++++++ academic/copasi/copasi.SlackBuild | 80 +++++++++++++++++++++++++++++++++++++++ academic/copasi/copasi.desktop | 8 ++++ academic/copasi/copasi.info | 10 +++++ academic/copasi/doinst.sh | 3 ++ academic/copasi/slack-desc | 19 ++++++++++ 6 files changed, 136 insertions(+) create mode 100644 academic/copasi/README create mode 100644 academic/copasi/copasi.SlackBuild create mode 100644 academic/copasi/copasi.desktop create mode 100644 academic/copasi/copasi.info create mode 100644 academic/copasi/doinst.sh create mode 100644 academic/copasi/slack-desc (limited to 'academic') diff --git a/academic/copasi/README b/academic/copasi/README new file mode 100644 index 000000000000..e32cb06d9c9d --- /dev/null +++ b/academic/copasi/README @@ -0,0 +1,16 @@ +COPASI is a package for modeling and simulation of biochemical networks, +popular in the field of systems biology. + +COPASI is a stand-alone program that simulates models of biochemical +networks using ODE solvers or Gillespie's stochastic simulation +algorithm. COPASI is compatible with models in SBML format. It also +performs several analyses, such as steady state, stability, parameter +sensitivity, elementary modes, Lyapunov exponents, optimization, and +parameter estimation. Data can be visualized in plots, histograms and +animations of network diagrams. COPASI's GUI is based on QT, but a +command line version is also included that allows for processing +computations in batch mode. + +COPASI is a collaboration between research groups at the Virginia +Bioinformatics Institute, University of Heidelberg, University of +Manchester and previously in the EML-Research. diff --git a/academic/copasi/copasi.SlackBuild b/academic/copasi/copasi.SlackBuild new file mode 100644 index 000000000000..3bd13424e4dc --- /dev/null +++ b/academic/copasi/copasi.SlackBuild @@ -0,0 +1,80 @@ +#!/bin/sh + +# Slackware build script for copasi + +# Copyright 2011 Pedro Mendes, Blacksburg, Virginia, USA +# 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=copasi +VERSION=35 +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +case "$(uname -m)" in + i?86) ARCH=i486 ;; + arm*) ARCH=arm ;; + *) ARCH=$(uname -m) ;; +esac + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i486" ]; then + BINNAME="Linux-Dynamic" +elif [ "$ARCH" = "x86_64" ]; then + BINNAME="Linux64-Dynamic" +else + echo "$ARCH is not supported by the $PRGNAM build script..." + exit 1 +fi + +# This is a repackage of a binary distribution +# CFLAGS are not required + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/Copasi-$VERSION-$BINNAME.tar.gz +mv $PRGNAM $PRGNAM-$VERSION +cd $PRGNAM-$VERSION +chown -R root:root . +chmod -R u+w,go+r-w,a-s . + +mkdir -p $PKG/usr/bin $PKG/usr/share/{copasi,pixmaps,applications} +cp -a bin/* $PKG/usr/bin/ +cp -r share/copasi $PKG/usr/share +cp $CWD/copasi.desktop $PKG/usr/share/applications/copasi.desktop +cp share/copasi/icons/Copasi48-Alpha.xpm $PKG/usr/share/pixmaps/copasi.xpm + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a LICENSE README $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +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/copasi/copasi.desktop b/academic/copasi/copasi.desktop new file mode 100644 index 000000000000..f58499422114 --- /dev/null +++ b/academic/copasi/copasi.desktop @@ -0,0 +1,8 @@ +[Desktop Entry] +Exec=COPASIDIR=/usr CopasiUI +Icon=/usr/share/pixmaps/copasi.xpm +Type=Application +Categories=Education;Science; +Name=COPASI +GenericName=Biochemical simulation +StartupNotify=true diff --git a/academic/copasi/copasi.info b/academic/copasi/copasi.info new file mode 100644 index 000000000000..43b4a01aa36e --- /dev/null +++ b/academic/copasi/copasi.info @@ -0,0 +1,10 @@ +PRGNAM="copasi" +VERSION="4.8.35" +HOMEPAGE="http://www.copasi.org" +DOWNLOAD="http://www.comp-sys-bio.org/mirror.copasi.org/Copasi-35-Linux-Dynamic.tar.gz" +MD5SUM="77446a83c0ce08fb62f0f735857bdd82" +DOWNLOAD_x86_64="http://www.comp-sys-bio.org/mirror.copasi.org/Copasi-35-Linux64-Dynamic.tar.gz" +MD5SUM_x86_64="671adba5851f76851499ba7ddb2253b5" +MAINTAINER="Pedro Mendes" +EMAIL="pedro@gepasi.org" +APPROVED="rworkman" diff --git a/academic/copasi/doinst.sh b/academic/copasi/doinst.sh new file mode 100644 index 000000000000..140e33222297 --- /dev/null +++ b/academic/copasi/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications +fi diff --git a/academic/copasi/slack-desc b/academic/copasi/slack-desc new file mode 100644 index 000000000000..ed42a91819c8 --- /dev/null +++ b/academic/copasi/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------------------------------------------------------| +copasi: COPASI (tool for modeling and simulation of biochemical networks) +copasi: +copasi: COPASI is a stand-alone program that simulates models of biochemical +copasi: networks using ODE solvers or Gillespie's stochastic simulation +copasi: algorithm. COPASI is compatible with models in SBML format. It also +copasi: performs several analyses: stability, parameter sensitivity, +copasi: elementary modes, Lyapunov exponents, optimization, and parameter +copasi: estimation. Data can be visualized in plots, histograms and animations +copasi: of network diagrams. Both GUI and a command line version are included. +copasi: +copasi: Homepage: http://www.copasi.org/ -- cgit v1.2.3