Metadata-Version: 2.1
Name: bioconda2biocontainer
Version: 0.0.1
Summary: Find biocontainer images for Bioconda packages
Home-page: https://github.com/BioContainers/bioconda2biocontainer
Author: Vera Alvarez, Roberto
Author-email: veraalva@ncbi.nlm.nih.gov
Maintainer: Vera Alvarez, Roberto
Maintainer-email: veraalva@ncbi.nlm.nih.gov
License: Public Domain
Project-URL: Documentation, https://github.com/BioContainers/bioconda2biocontainer/issues
Project-URL: Source, https://github.com/BioContainers/bioconda2biocontainer
Project-URL: Tracker, https://github.com/BioContainers/bioconda2biocontainer/issues
Description: # bioconda2biocontainer
        
        *bioconda2biocontainer* search the Biocontainer registry and return the image name
        for a Bioconda package. The images can be sorted by date, size or number of downloads.
        
        ## Basic usage
        
        ### Get latest image for bedtools version 2.27.0
        
        ```bash
        > bioconda2biocontainer --package_name bedtools --package_version 2.27.0
        quay.io/biocontainers/bedtools:2.27.0--he513fc3_4
        ```
        
        ### Get smaller image for bedtools version 2.27.0
        
        ```bash
        > bioconda2biocontainer --package_name bedtools --package_version 2.27.0 --sort_by_size
        quay.io/biocontainers/bedtools:2.27.0--he860b03_3
        ```
        
        ### Get image with more downloads for bedtools version 2.27.0
        
        ```bash
        > bioconda2biocontainer --package_name bedtools --package_version 2.27.0 --sort_by_download
        quay.io/biocontainers/bedtools:2.27.0--he860b03_3
        ```
        
        ### List all available images for bedtools version 2.27.0
        
        ```bash
        > bioconda2biocontainer --package_name bedtools --package_version 2.27.0 --all
        image	updated	size	downloads
        quay.io/biocontainers/bedtools:2.27.0--he513fc3_4	2019-10-26T00:00:00Z	17332806	0
        quay.io/biocontainers/bedtools:2.27.0--he860b03_3	2019-02-03T00:00:00Z	13482660	0
        quay.io/biocontainers/bedtools:2.27.0--he941832_2	2018-06-25T00:00:00Z	13652262	0
        quay.io/biocontainers/bedtools:2.27.0--1	2018-02-14T00:00:00Z	14094467	0
        quay.io/biocontainers/bedtools:2.27.0--0	2017-12-07T00:00:00Z	14087205	0
        ```
        
        ### List all available versions for bedtools
        
        ```bash
        > bioconda2biocontainer --package_name bedtools
        id	version	url
        bedtools-v2.28.0	v2.28.0	http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-v2.28.0
        bedtools-v2.27.1dfsg-4-deb	v2.27.1dfsg-4-deb	http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-v2.27.1dfsg-4-deb
        bedtools-v2.27.0	v2.27.0	http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-v2.27.0
        bedtools-v2.26.0dfsg-3-deb	v2.26.0dfsg-3-deb	http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-v2.26.0dfsg-3-deb
        bedtools-v2.25.0	v2.25.0	http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-v2.25.0
        bedtools-2.29.2	2.29.2	http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.29.2
        bedtools-2.29.1	2.29.1	http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.29.1
        bedtools-2.29.0	2.29.0	http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.29.0
        bedtools-2.28.0	2.28.0	http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.28.0
        bedtools-2.27.1	2.27.1	http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.27.1
        bedtools-2.27.0	2.27.0	http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.27.0
        bedtools-2.26.0gx	2.26.0gx	http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.26.0gx
        bedtools-2.25.0	2.25.0	http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.25.0
        bedtools-2.23.0	2.23.0	http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.23.0
        bedtools-2.22	2.22	http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.22
        bedtools-2.20.1	2.20.1	http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.20.1
        bedtools-2.19.1	2.19.1	http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.19.1
        bedtools-2.17.0	2.17.0	http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.17.0
        ```
        
        ## Install
        
        ```sh
        pip install bioconda2biocontainer
        ```
        
        For development:
        
        ```sh
        git clone https://github.com/BioContainers/bioconda2biocontainer
        cd bioconda2biocontainer
        pip install -r requirements/test.txt -e .
        ```
        
        ## Test
        
        Test configuration is defined in the `tox.ini` file and includes `py.test` tests
        and `flake8` source code checker.
        
        You can run all of the tests:
        
        ```
        python setup.py test
        ```
        
        To run just the `py.test` tests, not `flake8`, and to re-use the current `virtualenv`:
        
        ```sh
        py.test
        ```
        
        ## API
        
        ### Demo
        
        ```python
        >>> import json
        >>> from bioconda2biocontainer.biocontainer import find_package_by_name
        >>> tool = find_package_by_name('bedtools')
        >>> print(json.dumps(tool, indent=4))
        {
            "contains": [],
            "description": "Bedtools is an extensive suite of utilities for comparing genomic features in bed format.",
            "id": "bedtools",
            "identifiers": [
                "biotools:bedtools",
                "PMID:20110278"
            ],
            "license": "GPL-2.0",
            "name": "bedtools",
            "organization": "biocontainers",
            "pulls": 6111180,
            "tool_tags": [
                "genomics"
            ],
            "tool_url": "https://github.com/arq5x/bedtools2",
            "toolclass": {
                "description": "CommandLineTool",
                "id": "0",
                "name": "CommandLineTool"
            },
            "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools",
            "versions": [
                {
                    "id": "bedtools-v2.28.0",
                    "meta_version": "v2.28.0",
                    "name": "bedtools",
                    "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-v2.28.0"
                },
                {
                    "id": "bedtools-v2.27.1dfsg-4-deb",
                    "meta_version": "v2.27.1dfsg-4-deb",
                    "name": "bedtools",
                    "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-v2.27.1dfsg-4-deb"
                },
                {
                    "id": "bedtools-v2.27.0",
                    "meta_version": "v2.27.0",
                    "name": "bedtools",
                    "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-v2.27.0"
                },
                {
                    "id": "bedtools-v2.26.0dfsg-3-deb",
                    "meta_version": "v2.26.0dfsg-3-deb",
                    "name": "bedtools",
                    "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-v2.26.0dfsg-3-deb"
                },
                {
                    "id": "bedtools-v2.25.0",
                    "meta_version": "v2.25.0",
                    "name": "bedtools",
                    "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-v2.25.0"
                },
                {
                    "id": "bedtools-2.29.2",
                    "meta_version": "2.29.2",
                    "name": "bedtools",
                    "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.29.2"
                },
                {
                    "id": "bedtools-2.29.1",
                    "meta_version": "2.29.1",
                    "name": "bedtools",
                    "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.29.1"
                },
                {
                    "id": "bedtools-2.29.0",
                    "meta_version": "2.29.0",
                    "name": "bedtools",
                    "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.29.0"
                },
                {
                    "id": "bedtools-2.28.0",
                    "meta_version": "2.28.0",
                    "name": "bedtools",
                    "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.28.0"
                },
                {
                    "id": "bedtools-2.27.1",
                    "meta_version": "2.27.1",
                    "name": "bedtools",
                    "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.27.1"
                },
                {
                    "id": "bedtools-2.27.0",
                    "meta_version": "2.27.0",
                    "name": "bedtools",
                    "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.27.0"
                },
                {
                    "id": "bedtools-2.26.0gx",
                    "meta_version": "2.26.0gx",
                    "name": "bedtools",
                    "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.26.0gx"
                },
                {
                    "id": "bedtools-2.25.0",
                    "meta_version": "2.25.0",
                    "name": "bedtools",
                    "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.25.0"
                },
                {
                    "id": "bedtools-2.23.0",
                    "meta_version": "2.23.0",
                    "name": "bedtools",
                    "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.23.0"
                },
                {
                    "id": "bedtools-2.22",
                    "meta_version": "2.22",
                    "name": "bedtools",
                    "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.22"
                },
                {
                    "id": "bedtools-2.20.1",
                    "meta_version": "2.20.1",
                    "name": "bedtools",
                    "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.20.1"
                },
                {
                    "id": "bedtools-2.19.1",
                    "meta_version": "2.19.1",
                    "name": "bedtools",
                    "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.19.1"
                },
                {
                    "id": "bedtools-2.17.0",
                    "meta_version": "2.17.0",
                    "name": "bedtools",
                    "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.17.0"
                }
            ]
        }
        >>>
        
        ```
        
Keywords: Biocontainers
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: Public Domain
Classifier: Natural Language :: English
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
