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¶
Other old stable releases¶
- stable 2.0.x version v2.0.12.20150626
- stable 1.x version v1.40
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