Debian setup

# used by jenkins
apt-get install daemon
#apt-get install jenkins
apt-get install tomcat6
apt-get install tomcat6-admin
apt-get install curl
apt-get install r-base
apt-get install r-cran-rmysql

apt-get install texlive-xetex
apt-get install texlive-science
apt-get install texlive-latex-extra
apt-get install subversion
apt-get install cvs
apt-get install git
apt-get install wkhtmltopdf
apt-get install okular

apt-get install emacs23-nox

apt-get install jedit

apt-get install git-svn

apt-get install mailutils # smarthost

apt-get install graphviz


R
> install.packages("Rserve")
> install.packages("car") # may not be used
> install.packages("AER") #used by ParasiteClearance
> install.packages("DBI") #used by clinRepRep
> install.packages("RMySQL") #used by clinRepRep
>

Others currently installed on app-dev:
Cairo                   R graphics device using cairo graphics library
                        for creating high-quality bitmap (PNG, JPEG,
                        TIFF), vector (PDF, SVG, PostScript) and
                        display (X11 and Win32) output.
car                     Companion to Applied Regression
Formula                 Extended Model Formulas
lmtest                  Testing Linear Regression Models
sandwich                Robust Covariance Matrix Estimators
strucchange             Testing, Monitoring, and Dating Structural
                        Changes
zoo                     S3 Infrastructure for Regular and Irregular
                        Time Series (Z's ordered observations)


cairoDevice             Cairo-based cross-platform antialiased graphics
                        device driver.
Rserve                  Binary R server



chmod o+w /var/lib/tomcat6/webapps/

cp  /home/timp/.m2/repository/org/springframework/spring-instrument-tomcat/3.0.5.RELEASE/spring-instrument-tomcat-3.0.5.RELEASE.jar /usr/share/tomcat6/lib/

Ensure /etc/tomcat6/tomcat6-users.xml contains

<role rolename="poweruser" />
   <role rolename="poweruserplus" />
   <role rolename="probeuser" />
 
   <user username="admin" password="" roles="manager,admin" />

Get scrollbars in Eclipse:

 sudo su -c 'echo export LIBOVERLAY_SCROLLBAR=0 > /etc/X11/Xsession.d/80overlayscrollbars'

Get innotop working

perl -MCPAN -e shell
CPAN> install Term::ReadKey 

Ensure Rserve and Jenkins start at reboot

cd /etc/init.d
update-rc.d jenkins defaults
update-rc.d Rserve defaults

Set up networking.

Set up GMail as smart host for postfix.

Send me the IP address on boot.