Installation

tcrdist2 is designed to be run using Python 3. The latest version can be installed from GitHub using pip:

pip install git+https://github.com/kmayerb/tcrdist2.git@API2

Before installing tcrdist2, check that you have the appropriate dependencies.

Dependencies

tcrdist2 requires wheel, numpy, scipy, matplotlib, scipy, scikit-learn, tables, as well as the C-based sequence aligner parasail.

Analysis tools require pip installable dependencies: zipdist, tcrsampler, hierdiff, fishersapi, and pwseqdist.

Recommended python 3.6 dependencies are specified in the requirements36.txt . It should be placed the directory where you launch the installation.

pip install wheel
pip install -r requirements36.txt
pip install git+https://github.com/kmayerb/tcrdist2.git@API2

Virtual Env

You may want to use a virtual env to isolate tcrdist within its own environment. If you are creating a virtual environment on a Linux macine for the first time, the following preparatory steps may be required.

apt-get python3-dev
pip install virtualenv

With virtualenv installed, continue with the installation:

python3 -m venv ./venv
pip install wheel
source venv/bin/activate
pip install -r requirements36.txt
pip install git+https://github.com/kmayerb/tcrdist2.git@API2

Test the Installation

python -c 'import tcrdist as td; td.say_hello()'

You should see, the following:

Hello: 'By recombination, random insertion, deletion and substitution,
the small set of genes that encode the T-cell receptor has the potential
to create between 10^15 and 10^20 TCR clonotypes ...
However, the actual diversity of a persons TCR repertoire cannot possibly
lie in this range. There are only an estimated 10^13 cells in the
human body [3]' -- Laydon et al. 2015. PMC4528489

Optional Installation Files

To install important next-generation reference files:

python -c "import tcrdist as td; td.setup_db.install_all_next_gen()"

To install blast within your virtual environment (see Optional Blast Tools for installation on other platforms):

python -c "import tcrdist as td; td.setup_blast.install_blast_to_externals(download_from = 'ncbi_linux')"

Optional Blast Tools

tcrdist2 uses parasail for sequence alignments; however, some features have the option to use BLAST instead.

The BLAST version 2.2.16 used in Dash et al. 2017, can be optionally installed with the followings commands.

After installing tcrdist2, if working in a macOSX environment:

python -c "import tcrdist as td; td.setup_blast.install_blast_to_externals(download_from = 'ncbi_osx');"

After installing tcrdist2, if working in a Linux environment:

python -c "import tcrdist as td; td.setup_blast.install_blast_to_externals(download_from = 'ncbi_linux');"

If the NCBI links change, a backup download link can be accessed by changing the download_from argument:

python -c "import tcrdist as td; td.setup_blast.install_blast_to_externals(download_from = 'dropbox_osx');"

python -c "import tcrdist as td; td.setup_blast.install_blast_to_externals(download_from = 'dropbox_linux);"