Difference between revisions of "Transsys Installation"
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Before you go ahead installing transsys make sure the following dependencies are installed. Also make sure you use the development releases: | Before you go ahead installing transsys make sure the following dependencies are installed. Also make sure you use the development releases: | ||
| − | *python | + | *python. Don't forget to setup PYTHONPATH (e.g. export PYTHONPATH=/usr/local/lib/python2.7) |
*R | *R | ||
*Open GL (If you're planning to use L-Transsys) | *Open GL (If you're planning to use L-Transsys) | ||
Revision as of 04:22, 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 (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
