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 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 | ||
| Line 26: | Line 26: | ||
== Test == | == Test == | ||
| + | |||
| + | You can test whether the installation was successful by trying the command | ||
| + | |||
| + | transexpr testdata/check.tra | ||
| + | |||
| + | in the <code>transsys-current</code> directory. You should see a table of numbers (100 rows, plus one header), representing the gene expression dynamics of the transsys program in the <code>check.tra</code> 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 ../../ | ||
| + | |||
| + | * have_glut: no | ||
| + | Make sure OPEN GL and GLUT are installed (both dev options). | ||
Latest revision as of 09:31, 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 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 ../../
- have_glut: no
Make sure OPEN GL and GLUT are installed (both dev options).
