Metadata-Version: 2.1
Name: htsinfer
Version: 0.2.0
Summary: HTSinfer infers metadata from High Throughput Sequencing (HTS) data
Home-page: https://github.com/zavolanlab/htsinfer
Author: Rohan Kandhari
Author-email: rohan.kandhari.bme16@iitbhu.ac.in
Maintainer: Rohan Kandhari
Maintainer-email: rohan.kandhari.bme16@iitbhu.ac.in
License: UNKNOWN
Project-URL: Repository, https://github.com/zavolanlab/htsinfer
Project-URL: Tracker, https://github.com/zavolanlab/htsinfer/issues
Description: # HTSinfer
        
        [![license][badge-license]][badge-url-license]
        [![CI][badge-ci]][badge-url-ci]
        [![coverage][badge-coverage]][badge-url-coverage]
        
        HTSinfer infers metadata from High Throughput Sequencing (HTS) data
        
        ## Usage
        
        ```sh
        htsinfer [-hv]
        ```
        
        ## Parameters
        
        ```console
        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:
        
        ```sh
        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`][res-virtualenv].
        
        To verify the correct installation, you can run the tests that are shipped with
        the package:
        
        ```sh
        python -m pytest
        ```
        
        You can then run the package via the CLI script `htsinfer` as described in the
        [Usage](#Usage) section.
        
        ### Run inside container
        
        If you have [Docker][res-docker] installed, you can also pull the Docker
        image:
        
        ```sh
        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:
        
        ```sh
        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](CONTRIBUTING.md) if you are interested to
        contribute. Please mind the [code of conduct](CODE_OF_CONDUCT.md) for all
        interactions with the community.
        
        ## Contact
        
        For questions or suggestions regarding the code, please use the
        [issue tracker][res-issue-tracker]. For any other inquiries, please contact us
        by email: <zavolab-biozentrum@unibas.ch>
        
        (c) 2020 [Zavolan lab, Biozentrum, University of Basel][res-zavolab]
        
        [badge-ci]: <https://travis-ci.com/zavolanlab/htsinfer.svg?branch=master>
        [badge-coverage]: <https://img.shields.io/coveralls/github/zavolanlab/htsinfer/master>
        [badge-license]: <https://img.shields.io/badge/license-Apache%202.0-orange.svg?style=flat&color=important>
        [badge-url-ci]: <https://travis-ci.com/zavolanlab/htsinfer>
        [badge-url-coverage]: <https://coveralls.io/github/zavolanlab/htsinfer>
        [badge-url-license]: <http://www.apache.org/licenses/LICENSE-2.0>
        [res-docker]: <https://www.docker.com/>
        [res-docker-vol]: <https://docs.docker.com/storage/volumes/>
        [res-issue-tracker]: <https://github.com/zavolanlab/htsinfer/issues>
        [res-virtualenv]: <https://virtualenv.pypa.io/en/latest/>
        [res-zavolab]: <https://zavolan.biozentrum.unibas.ch/>
        
Keywords: bioinformatics,ngs,high-throughput sequencing,inference
Platform: UNKNOWN
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Utilities
Description-Content-Type: text/markdown
