Download and Install¶
Install using pip¶
sudo pip install transvar
pip install --user transvar
to upgrade from a previous version
pip install -U transvar
Try out the docker image¶
Also try out using the pre-built docker image Assuming the existence of ~/references/hg38/hg38.fa and ~/references/hg38/hg38.fa.fai
docker pull zhouwanding/transvar:2.4.6 docker run -v ~/references/hg38:/data -ti zhouwanding/transvar:2.4.6 transvar panno -i PIK3CA:p.E545K --ensembl --reference /data/hg38.fa
Download the program¶
The only requirement for building TransVar are Python 2.7 and a reasonably modern C compiler such as gcc.
Install from source¶
python setup.py install --prefix [folder]
The installation will create two subfolders:
[folder]/lib (which would contain libraries) and
[folder]/bin (which would contain transvar executable).
When you run transvar, make sure
[folder]/lib/python2.7/site-packages is in your PYTHONPATH. In some occasions, you need to
mkdir -p [folder]/lib/python2.7/site-packages to make sure it exists before you could run
You can add it by putting
.profile depending on your OS.
The installed executable is [folder]/bin/transvar.
System-wise install (need root)¶
sudo python setup.py install