# callingCardsTools
[](https://doi.org/10.5281/zenodo.10042067)
[](https://github.com/cmatKhan/callingCardsTools/actions/workflows/codecov.yml)
[](http://bioconda.github.io/recipes/callingcardstools/README.html)
## Introduction
`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](https://github.com/nf-core/callingcards) pipeline,
which provides a workflow to process both yeast and mammals Calling Cards data.
## Documentation
[Served Documentation](https://cmatkhan.github.io/callingCardsTools/) provides
information on filetypes and the API. For help with the cmd line tools,
simply install callingcardstools (see below) and do:
```bash
callingcardstools --help
```
Each of the cmd line tools also provides a `--help` message.
## Installation
callingCardsTools is available through bioconda:
```bash
conda install -c bioconda callingcardstools
```
pypi:
```bash
pip install callingcardstools
```
or github (this will be the most current version):
```bash
pip install git+https://github.com/cmatkhan/callingCardsTools.git
```
After installing, you can get help with the cmd line tools by doing:
```bash
callingcardstools --help
```
## Callingcardstools is containerized:
- A singularity container is hosted on
[Galaxyhub](https://depot.galaxyproject.org/singularity/). 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)](https://quay.io/repository/biocontainers/callingcardstools).
Again, make sure you get the correct version.
## Development Installation
1. install [poetry](https://python-poetry.org/)
- 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`
2. git clone the repo
3. cd into the repo and issue the command `poetry install`
4. shell into the virtual environment with `poetry shell`
5. 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.
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