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. .. 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

Current release

Latest release is available here

For all previous versions, see here

Other old stable releases

Dependency

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 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 setup.py. 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 setup.py install