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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]] #WiKi ---+++ Wiki * [[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]] * 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>
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Topic revision: r103 - 21 Aug 2017,
DalePlummer
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