HTSinfer

HTSinfer infers metadata from High Throughput Sequencing (HTS) data

Usage

htsinfer [-hv]

Parameters

optional arguments:
  -h, --help     show this help message and exit
  --version      show version information and exit
  -v, --verbose  print logging messages to STDERR
  --debug        also print debugging messages to STDERR

Extended usage

Run locally

In order to use the package, clone the repository and install the dependencies:

git clone https://github.com/zavolanlab/htsinfer
cd htsinfer
pip install -r requirements.txt
python setup.py install

NOTE: You may want to install dependencies inside a virtual environment, e.g., using virtualenv.

To verify the correct installation, you can run the tests that are shipped with the package:

python -m pytest

You can then run the package via the CLI script htsinfer as described in the Usage section.

Run inside container

If you have Docker installed, you can also pull the Docker image:

docker pull zavolab/htsinfer:latest

The script can be found in directory /home/user/htsinfer/src inside the Docker container.

The Docker image contains an entry point for the CLI script htsinfer so that you can run it, e.g., with:

docker run --rm -it zavolab/htsinfer:latest --help

NOTE: To run the tool on your own data in that manner, you will probably need to [mount a volume][res-docker-volume] to allow the container read input files and write persistent output from/to the host file system.

Contributing

This project lives off your contributions, be it in the form of bug reports, feature requests, discussions, or fixes and other code changes. Please refer to the contributing guidelines if you are interested to contribute. Please mind the code of conduct for all interactions with the community.

Contact

For questions or suggestions regarding the code, please use the issue tracker. For any other inquiries, please contact us by email: zavolab-biozentrum@unibas.ch

(c) 2020 Zavolan lab, Biozentrum, University of Basel