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---++ Department Computing Operations

   * [[FrequentlyAskedQuestionsFAQ][Frequently Asked Questions (FAQ)]]
   * [[Main.GettingStartedBiostatistics][Getting Started at Vanderbilt Biostatistics]] (includes IT information)
   * [[LinuxWorkshops][Linux Workshops]]
   * [[FormatPolicies][Department File Format Policies]]
   * StatCompServerInfo
   * [[SoftMakerOffice2012][SoftMaker Office 2012]]
 
---+++ Data Transmission
   * [[https://it.vanderbilt.edu/security/secure-communications/secure-file-transfer.php][Secure File Transfer]]
   * [[Main.DataHippo][The Data-Hippo Secure Data Transfer Application]]

#WorkstationSetup
---+++ Linux Workstation Setup
   * [[Main.UbuntuSetup][User workstation setup and configuration]]
   * Recommended [[FolderOrg][directory and e-mail folder organization]]
   * NotesOnUdev
   * MappingBiostatShares
   * MappingVanderbiltShares
   * [[VendorInstall][Instructions to vendor for workstation configuration]]
   * How to [[SystemScriptHowto][create system scripts]]
   * [[SylpheedWentAway][Old sylpheed instructions]]

#DatabaseProject
---+++ Database Project
   * [[ProDevGrantDBProject][Database specification]]
   * [[Research Database Goals]]

#WebCalendar
---+++ Webcalendar 

   * [[WebCalendar][WebCalendar instructions and help]]

#TWiKi
---+++ Twiki  

   * [[HintsTwiki][Hints and help for using and editing the Twiki]]
   * [[UserpageTemplate][A template for the user page]]
   * [[Twiki Access Discussion]]
   * HtmlToTwiki

#CvS
---+++ CVS

   * [[BiostatCvs][Information on the Biostat CVS Server]]
   * [[http://biostat.mc.vanderbilt.edu/cgi-bin/cvsweb.cgi][CVSWeb]] -- Browse the Biostat CVS Server

#PeRl
---+++ RSPerl

   * RSPerl is an R module that works with Perl.  With it you can run R commands inside Perl and vice versa.  Below are the instructions to get the Perl module working (so you can run R from Perl scripts).
   * *Note*: you must recompile R from the source, since RSPerl requires R's shared library.  Below are instructions on how to do this.
      * make a directory in your home folder for the R source file (ex: /home/vunetid/src) by running "mkdir /home/vunetid/src"
      * change your current directory to the one you just created
      * download the R source files by running "wget http://www.biometrics.mtu.edu/CRAN/src/base/R-2/R-2.1.1.tar.gz" or by grabbing them from a mirror on the [[http://www.r-project.org][R website]]
      * unzip the tarball by running "tar -xvzf R-2.1.1.tar.gz"
      * cd into the R directory ("cd R-2.1.1")
      * run: CFLAGS="-g" CXXFLAGS="-g" FFLAGS="-g" ./configure --enable-R-shlib
      * then run "make" (but don't run "make install", this will leave the R files in your home directory)
      * now it's time to install RSPerl
   * Download the source code (RSPerl_x.x-x.tar.gz) from the [[http://www.omegahat.org/RSPerl/][RSPerl]] website.
   * Install by running "R CMD INSTALL -c -l /home/vunetid/src/R-2.1.1/library --configure-args='--with-in-perl' RSPerl_x.x-x.tar.gz" 
   * Edit your ~/.bashrc file and add the following lines:
      * export R_LIBS="/home/vunetid/src/R-2.1.1/library/"
      * export PATH="/home/vunetid/src/R-2.1.1/bin:$PATH"
      * export PERLLIB="/home/vunetid/src/R-2.1.1/library/RSPerl/share/blib/arch:/home/vunetid/src/R-2.1.1/library/RSPerl/share/blib/lib:/home/vunetid/src/R-2.1.1/library/RSPerl/scripts"
      * export LD_LIBRARY_PATH="/home/vunetid/src/R-2.1.1/bin:/home/vunetid/src/R-2.1.1/lib"
      * export R_HOME="/home/vunetid/src/R-2.1.1"
   * Reload your .bashrc by running "source ~/.bashrc"
   * Test to make sure your installation was successful by running "perl ~/src/R-2.1.1/library/RSPerl/scripts/test.pl"
   * If you have any questions, please ask Main.JeremyStephens.  Good luck!

#SystemImaging
---+++ System Imager
   * Using SystemImager to provide our own system images

#PdfIng
---+++ Viewing and Changing =PDF= Documents
   * Recommended PDF readers: =okular=, =kpdf=, =xpdf= (not fancy but extremely fast), =[[FrequentlyAskedQuestionsFAQ#How_do_I_Install_Acrobat_Reader][acroread]]=, =gpdf=
   * [[PdfAnnotation][Annotating]] PDF documents
   * [[PdfManip][Manipulating]] PDF documents

#PrintIng
---+++ Printing
   * [[PhaserNotes][Instructions for setting up access to the Xerox Phaser 6250 DP color laser printer]]
   * [[CupsNotes][Various CUPS Knowlege]]

#EditingTools
---+++ Editors
   * [[EmacsLaTeXTools][Emacs]]
   * [[Geany][Geany]]

#LinuxQuestions
---+++ Linux
   * [[ComputingErSol][Various Linux Errors & Solutions]]
   * [[InstallXtraFonts][Installing extra languages for KDE]]
   * [[LinuxLinks][Linux related web links]] (distribution ISOs, apt repository, etc)
   * [[LinuxUserEfficient][Improving User Efficiency]]
   * [[LinuxUserSurveyDraft][User Survey Draft]]
   * [[http://www.tuxmagazine.com/node/1000020][Konqueror Web Shortcuts]], for web browsing
   * [[http://nlug.wikispot.org][Nashville Linux Users Group]]

#LaTex
---+++ <nop>LaTex Links and Notes | See also DocProcess
   * [[http://www.stdout.org/~winston/latex/][LaTex cheat sheet]]
   * [[http://www.giss.nasa.gov/latex/][a nice LaTex help page]] from someone at NASA
   * Problems with updating !LaTeX (tetex-bin)
The tetex-bin debian file can sometimes be difficult to update.  Part of the reason are "ls-R" files that contain various path information.  They are in such places as "/var/cache/fonts", "/var/lib/texmf", and "/usr/share/texmf".  Try deleting these files and running either *mktexlsr* or *texhash* in those directories.  Then reconfigure tetex-bin with the command *dpkg-reconfigure tetex-bin*.
   * Commands to invoke <nop>LaTex and view or print the output:
    <verbatim>
    Linux
    $ latex test.tex   # invokes LaTex, processes test.tex, and writes test.dvi
    $ kdvi test.dvi    # opens test.dvi for viewing and printing

    Windows (MiKTex)
    > latex test.tex
    > yap test.tex
    </verbatim>
Topic revision: r102 - 18 Jun 2015, DalePlummer
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