Difference between revisions of "Transsys Installation"
Line 5: | Line 5: | ||
*python. Don't forget to setup PYTHONPATH (e.g. export PYTHONPATH=/usr/local/lib/python2.7) | *python. Don't forget to setup PYTHONPATH (e.g. export PYTHONPATH=/usr/local/lib/python2.7) | ||
*R | *R | ||
− | *Open GL and GLUT (If you're planning to use L-Transsys) | + | *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 | *Flex | ||
*Bison | *Bison |
Revision as of 09:21, 5 March 2015
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 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 ../../