Download and Install¶
Install using pip¶
sudo pip install transvar
pip install --user transvar
to upgrade from a previous version
pip install -U transvar
Use the docker images¶
The pre-built docker image is easy to try out. The docker images can be found here
Assuming the existence of ~/references/hg38/hg38.fa and ~/references/hg38/hg38.fa.fai.
Without downloading anything, the transvar docker has pre-built hg38 annotation. .. code:: bash
docker run -v ~/references/hg38:/ref -ti zhouwanding/transvar:latest transvar panno -i PIK3CA:p.E545K –ensembl –reference /ref/hg38.fa
To use other genome build, one needs to download annotations. Here I am using ~/test as an example of local path for storing the transvar annotations. Note that this local path needs be imaged to /anno inside the docker image. This is done by (showing hg19) .. code:: bash
docker run -v ~/test:/anno -ti zhouwanding/transvar:latest transvar config –download_anno –refversion hg19 –skip_reference
Now one can use hg19, but note again one needs to image the path of downloaded annotation to /anno. One also needs the fa-indexed reference. .. code:: bash
docker run -v ~/test:/anno -v ~/references/hg19:/ref -ti zhouwanding/transvar:latest transvar panno -i PIK3CA:p.E545K –ensembl –reference /ref/hg19.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