Transsys Installation

Pre-requisites

Before you go ahead installing transsys make sure the following dependencies are installed. Also make sure you use the development releases:

• python. Don't forget to setup PYTHONPATH (e.g. export PYTHONPATH=/usr/local/lib/python2.7)
• R
• Open GL and GLUT (If you're planning to use L-Transsys). For Ubuntu users sometimes you need to libgle3-dev and libgtkglext1-dev in addition to freeglut-dev
• Flex
• Bison

Download package

• Download transsys from http://www.transsys.net/software/transsys-current.tar.gz
• Unpack the tar file (e.g. tar -zxvf transsys-current.tar.gz)
• Change to newly created transsys directory (e.g cd transsys_curreny )

Installing transsys

Issue the three following commands one by one:

• 'configure'. We recommend you use ./configure --help to see how the command works.
• 'make'
• 'make install'. Before you issue this command make sure the directory '/lib/R' exists in your home directory. Otherwise you need to create it and export it (e.g. export R_LIBS=${HOME}/yourdirectory/lib/R). Also, you need to install the R packahe 'xpipe' which you can find here: http://www.transsys.net/software/xpipe_0.1.tar.gz. Use 'R CMD INSTALL xpipe_0.1.tar.gz' to install the package.

A succesful installation will not show any errors.

Test

You can test whether the installation was successful by trying the command

 transexpr testdata/check.tra

in the transsys-current directory. You should see a table of numbers (100 rows, plus one header), representing the gene expression dynamics of the transsys program in the check.tra file. If you

• To test whether the Python API is ready. Run python and import transsys. Yo shouldn't get any errors.
• To test ltransgl, go to testdata (cd testdata) and execute the following command: ltransgl defglo.trl

You shouldn't errors if the installation is correct. Otherwise make sure you install the software necessary. Please also go to the ltransgl to learn how to use l-transsys

Troubleshooting

• ERROR: a 'NAMESPACE' file is required xpipe_0.1.tar.gz

do: tar -xzvf xpipe_0.1.tar.gz cd xpipe echo 'exportPattern( "." )' > NAMESPACE cd .. tar -zcf xpipe_0.1.tar.gz xpipe

• ERROR: a 'NAMESPACE' file is required

cd toolbox/transsys echo 'exportPattern( "." )' > NAMESPACE cd ../../

cd toolbox/transarr echo 'exportPattern( "." )' > NAMESPACE cd ../../