161 lines
6.8 KiB
TeX
161 lines
6.8 KiB
TeX
\documentclass[titlepage,11pt]{article}
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\textwidth 6.5in
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\textheight 9in
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\oddsidemargin -0.2in
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\topmargin -0.5in
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\usepackage{indentfirst,graphics,alltt,epsfig,color}
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\title{iBioSim Installation Instructions}
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\author{Chris J. Myers}
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% \date{Created: August 11th, 2008\\
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% Last Revised: August 14th, 2008
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% }
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\begin{document}
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\maketitle
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%show only subsection granularity in the toc
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%\setcounter{tocdepth}{2}
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\tableofcontents
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\clearpage
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%\setlength{\parindent}{0em}
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%\setlength{\parskip}{10pt}
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\section{General Requirements}
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\noindent
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There are versions of {\tt iBioSim} available for Windows, Linux, and
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MacOS. You can download the appropriate installation file from:\\
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%%tth:\begin{html}<a href="http://www.async.ece.utah.edu/iBioSim/">\end{html}
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{\tt http://www.async.ece.utah.edu/iBioSim}.
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%%tth:\begin{html}</a>\end{html}
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{\tt iBioSim} requires that you have
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%%tth:\begin{html}<a href="http://java.sun.com/javase/downloads/index.jsp">\end{html}
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Java Runtime Environment 1.6
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%%tth:\begin{html}</a>\end{html}
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or higher install on your system. It is also useful to have
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%%tth:\begin{html}<a href="http://www.graphviz.org/">\end{html}
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Graphviz.
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%%tth:\begin{html}</a>\end{html}
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Also, you should associate files with a ``.dot'' extension with the
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{\tt Graphviz} tool, and files with the ``.xhtml'' extension to your
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web browswer. There is also a pure java version available that
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supports most though not all features of {\tt iBioSim}. This is a good option when having trouble with the other installations, since it is machine independent.
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\section{Java Installation}
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\noindent
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To install the pure Java version, you need to download {\tt iBioSim-2.8-Java.zip} and unzip it in the directory you wish to install. The {\tt iBioSim.jar} file should be executable, but may require being invoked using the explicit command: {\tt java -jar iBioSim.jar}.
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The {\tt iBioSim.mac64} script makes it look better on Mac environment.
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\section{MacOS Installation}
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\noindent
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To install on MacOS, you need to download {\tt
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iBioSim-$\langle$version$\rangle$-MacOS.dmg} file. You should then
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open this file with {\tt DiskImageMounter.app}. This should open up
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this disk image in {\tt finder}. You should then copy the contents of
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this disk image to your Applications folder. You should then be able
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to start {\tt iBioSim} by double-clicking on this application.
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\section{Windows Installation}
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\noindent
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Download and execute {\tt iBioSim-$\langle$version$\rangle$-Setup.exe}.\\
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The installation uses InstallJammer. It first asks you for your
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preferred installation language. Make your selection and press {\tt OK}.
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\includegraphics[height=40mm]{screenshots/language}
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The next screen tells you that you what version you are installing.
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Press {\tt Next} to continue.
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\includegraphics[height=95mm]{screenshots/setup}
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Next, it ask you for an installation location. Please make sure to
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select a path that does not have any spaces or special symbols as
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these cause problems with {\tt iBioSim}.
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\includegraphics[height=95mm]{screenshots/location}
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You are now ready to install. Press {\tt Next} to continue.
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\includegraphics[height=95mm]{screenshots/confirm}
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You are all done. Press {\tt Finish}. If selected, {\tt iBioSim}
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will launch immediately. Otherwise, you can start it using your
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desktop shortcut or from your start menu.
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\includegraphics[height=95mm]{screenshots/finish}
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In your start menu, there should be an option to uninstall. If you
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select this, it will ask if you are sure then proceed to completely
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remove {\tt iBioSim} from your system. It is highly recommended that
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you remove {\tt iBioSim} using this uninstall procedure before
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installing a new version.
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\section{Linux Installation}
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\noindent
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Since InstallJammmer is also used for the Linux install, the
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installation instructions are essentially the same.
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First, download {\tt iBioSim-$\langle$version$\rangle$-Linux-x86\_64-Install}.
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Open a terminal and browse to where this file was download. You must
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make this file executable:\\
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{\tt chmod u+x iBioSim-$\langle$version$\rangle$-Linux-x86\_64-Install}.
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You should then execute this file:\\
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{\tt ./iBioSim-$\langle$version$\rangle$-Linux-x86\_64-Install}.
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This starts InstallJammer. It first asks you for your
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preferred installation language. Make your selection and press {\tt OK}.
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\includegraphics[height=40mm]{screenshots/language}
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The next screen tells you that you what version you are installing.
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Press {\tt Next} to continue.
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\includegraphics[height=95mm]{screenshots/setup}
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Next, it ask you for an installation location. Please make sure to
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select a path that does not have any spaces or special symbols as
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these cause problems with {\tt iBioSim}.
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\includegraphics[height=95mm]{screenshots/location}
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You are now ready to install. Press {\tt Next} to continue.
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\includegraphics[height=95mm]{screenshots/confirm}
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You are all done. Press {\tt Finish}. If selected, {\tt iBioSim}
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will launch immediately. Otherwise, you can start it using your
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desktop shortcut or from your start menu.
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\includegraphics[height=95mm]{screenshots/finish}
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In your start menu, there should be an option to uninstall. If you
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select this, it will ask if you are sure then proceed to completely
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remove {\tt iBioSim} from your system. It is highly recommended that
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you remove {\tt iBioSim} using this uninstall procedure before
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installing a new version.
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Note that since there are a large number of different linux installations, there can be problems especially with older installations. If you are having problems though, first log out and back in. There are some environment variables that need to be set. If you are still having problems, then read on.
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Our linux installations are currently built for 32-bit and 64-bit versions of Fedora 15. While the Java parts of our program port smoothly, there are often issues with the dynamic libraries and the C/C++ programs {\tt reb2sac} and {\tt GeneNet}. If you are having a problem, the first step is to download and build libsbml Version 5.0. You will need to replace the libsbml.so* and libsbmlj.so files with your build of libsbml in either lib or lib64 depending on whether you are using a 32-bit or 64-bit machine. At this point, you should be able to start {\tt iBioSim}. However, if you are still having problems, send an email to {\tt myers@ece.utah.edu} including information about your OS and any error messages when you try to execute {\tt iBioSim} from the command line.
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You should also now test {\tt reb2sac} and {\tt GeneNet}. In your install directory, try the following:
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\begin{itemize}
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\item cd bin
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\item export LD\_LIBRARY\_PATH=\$BIOSIM/lib:\$LD\_LIBRARY\_PATH \\
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Note that this is for bash shell, so you may need to change for your shell, if not bash.
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\item ./reb2sac
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\item ./GeneNet
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\end{itemize}
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You should see the usage lines for these programs. If you do not, you may need custom builds, contact {\tt myers@ece.utah.edu}.
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\end{document}
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