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 (If you're planning to use L-Transsys)
• 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 the

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 ../../