academic/copasi: Added (modeling/simulation of biochemical networks)
Signed-off-by: Robby Workman <rworkman@slackbuilds.org>
This commit is contained in:
Pedro Mendes
Robby Workman
parent
d74ce3a23f
commit
9639f2f744
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COPASI is a package for modeling and simulation of biochemical networks,
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popular in the field of systems biology.
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COPASI is a stand-alone program that simulates models of biochemical
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networks using ODE solvers or Gillespie's stochastic simulation
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algorithm. COPASI is compatible with models in SBML format. It also
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performs several analyses, such as steady state, stability, parameter
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sensitivity, elementary modes, Lyapunov exponents, optimization, and
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parameter estimation. Data can be visualized in plots, histograms and
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animations of network diagrams. COPASI's GUI is based on QT, but a
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command line version is also included that allows for processing
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computations in batch mode.
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COPASI is a collaboration between research groups at the Virginia
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Bioinformatics Institute, University of Heidelberg, University of
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Manchester and previously in the EML-Research.
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#!/bin/sh
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# Slackware build script for copasi
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# Copyright 2011 Pedro Mendes, Blacksburg, Virginia, USA
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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PRGNAM=copasi
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VERSION=35
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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case "$(uname -m)" in
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i?86) ARCH=i486 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$(uname -m) ;;
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esac
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CWD=$(pwd)
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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if [ "$ARCH" = "i486" ]; then
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BINNAME="Linux-Dynamic"
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elif [ "$ARCH" = "x86_64" ]; then
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BINNAME="Linux64-Dynamic"
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else
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echo "$ARCH is not supported by the $PRGNAM build script..."
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exit 1
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fi
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# This is a repackage of a binary distribution
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# CFLAGS are not required
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set -e
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $PRGNAM-$VERSION
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tar xvf $CWD/Copasi-$VERSION-$BINNAME.tar.gz
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mv $PRGNAM $PRGNAM-$VERSION
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cd $PRGNAM-$VERSION
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chown -R root:root .
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chmod -R u+w,go+r-w,a-s .
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mkdir -p $PKG/usr/bin $PKG/usr/share/{copasi,pixmaps,applications}
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cp -a bin/* $PKG/usr/bin/
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cp -r share/copasi $PKG/usr/share
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cp $CWD/copasi.desktop $PKG/usr/share/applications/copasi.desktop
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cp share/copasi/icons/Copasi48-Alpha.xpm $PKG/usr/share/pixmaps/copasi.xpm
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a LICENSE README $PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cat $CWD/doinst.sh > $PKG/install/doinst.sh
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
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[Desktop Entry]
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Exec=COPASIDIR=/usr CopasiUI
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Icon=/usr/share/pixmaps/copasi.xpm
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Type=Application
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Categories=Education;Science;
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Name=COPASI
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GenericName=Biochemical simulation
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StartupNotify=true
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PRGNAM="copasi"
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VERSION="4.8.35"
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HOMEPAGE="http://www.copasi.org"
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DOWNLOAD="http://www.comp-sys-bio.org/mirror.copasi.org/Copasi-35-Linux-Dynamic.tar.gz"
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MD5SUM="77446a83c0ce08fb62f0f735857bdd82"
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DOWNLOAD_x86_64="http://www.comp-sys-bio.org/mirror.copasi.org/Copasi-35-Linux64-Dynamic.tar.gz"
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MD5SUM_x86_64="671adba5851f76851499ba7ddb2253b5"
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MAINTAINER="Pedro Mendes"
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EMAIL="pedro@gepasi.org"
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APPROVED="rworkman"
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if [ -x /usr/bin/update-desktop-database ]; then
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/usr/bin/update-desktop-database -q usr/share/applications
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fi
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@ -0,0 +1,19 @@
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description. Line
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# up the first '|' above the ':' following the base package name, and the '|'
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# on the right side marks the last column you can put a character in. You must
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# make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':' except on otherwise blank lines.
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|-----handy-ruler------------------------------------------------------|
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copasi: COPASI (tool for modeling and simulation of biochemical networks)
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copasi:
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copasi: COPASI is a stand-alone program that simulates models of biochemical
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copasi: networks using ODE solvers or Gillespie's stochastic simulation
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copasi: algorithm. COPASI is compatible with models in SBML format. It also
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copasi: performs several analyses: stability, parameter sensitivity,
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copasi: elementary modes, Lyapunov exponents, optimization, and parameter
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copasi: estimation. Data can be visualized in plots, histograms and animations
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copasi: of network diagrams. Both GUI and a command line version are included.
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copasi:
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copasi: Homepage: http://www.copasi.org/
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