Download and Install

Install using pip

sudo pip install transvar

or locally

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.

docker run -v ~/references/hg38:/ref 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):

docker run -v ~/test:/anno 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.

docker run -v ~/test:/anno -v ~/references/hg19:/ref
   zhouwanding/transvar:latest transvar panno -i PIK3CA:p.E545K
   --ensembl --reference /ref/hg19.fa

Download the program

Current release

Latest release is available here

For all previous versions, see here

Other old stable releases


The only requirement for building TransVar are Python 2.7 and a reasonably modern C compiler such as gcc.

Install from source

Local install

python 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

export PYTHONPATH=$PYTHONPATH:[folder]/lib/python-2.7/site-packages/

to your .bashrc or .profile depending on your OS.

The installed executable is [folder]/bin/transvar.

System-wise install (need root)

sudo python install