CallingCardsTools Provides both an API and a number of cmd line tools
for processing raw Calling Cards data. This is used in the
nf-core/callingcards pipeline,
which provides a workflow to process both yeast and mammals Calling Cards data.
Served Documentation provides information on filetypes and the API. For help with the cmd line tools, simply install callingcardstools (see below) and do:
callingcardstools --helpEach of the cmd line tools also provides a --help message.
callingCardsTools is available through bioconda:
conda install -c bioconda callingcardstoolspypi:
pip install callingcardstoolsor github (this will be the most current version):
pip install git+https://github.com/cmatkhan/callingCardsTools.gitAfter installing, you can get help with the cmd line tools by doing:
callingcardstools --help-
A singularity container is hosted on Galaxyhub. If you go to this site, make sure the 'c's have loaded and then search for 'callingcardstools'. There is a container for each version which is on bioconda. Make sure you get the correct version.
-
A docker container is hosted on quay (and biocontainers). Again, make sure you get the correct version.
- install poetry
- I prefer to set the default location of the virtual environment to the
project directory. You can set that as a global configuration for your
poetry installation like so:
poetry config virtualenvs.in-project true
-
git clone the repo
-
cd into the repo and issue the command
poetry install -
shell into the virtual environment with
poetry shell -
you can
pip install -e .to install the package in editable mode. This is useful if you want to test the cmd line interface as you make changes to the source code.