Metadata-Version: 2.1
Name: bioconda2biocontainer
Version: 0.0.3
Summary: Tools to synchronize bioconda packages and versions with Biocontainer images
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
        
        ![Python package](https://github.com/BioContainers/bioconda2biocontainer/workflows/Python%20package/badge.svg)
        
        *bioconda2biocontainer* includes a series of python scripts and API to query
        the Biocontainer registry.
        
        ## Scripts
        
        ### *bioconda2biocontainer*
        
        This script 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.
        
        Option **container_type** can be: Docker, Singularity or Conda
        
        #### 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	container_type
        https://depot.galaxyproject.org/singularity/bedtools:2.27.0--he513fc3_4	2019-10-27T05:29:00Z	17178624	0	Singularity
        quay.io/biocontainers/bedtools:2.27.0--he513fc3_4	2019-10-26T00:00:00Z	17332806	0	Docker
        https://depot.galaxyproject.org/singularity/bedtools:2.27.0--0	2019-08-27T18:20:00Z	13885440	0	Singularity
        https://depot.galaxyproject.org/singularity/bedtools:2.27.0--1	2019-08-01T21:40:00Z	13889536	0	Singularity
        https://depot.galaxyproject.org/singularity/bedtools:2.27.0--he860b03_3	2019-08-01T21:40:00Z	13389824	0	Singularity
        https://depot.galaxyproject.org/singularity/bedtools:2.27.0--he941832_2	2019-08-01T21:40:00Z	13549568	0	Singularity
        quay.io/biocontainers/bedtools:2.27.0--he860b03_3	2019-02-03T00:00:00Z	13482660	0	Docker
        quay.io/biocontainers/bedtools:2.27.0--he941832_2	2018-06-25T00:00:00Z	13652262	0	Docker
        bedtools==2.27.0--he860b03_3	2018-06-24T00:00:00Z	1129407	35562	Conda
        bedtools==2.27.0--0	2018-06-24T00:00:00Z	1129407	35562	Conda
        bedtools==2.27.0--1	2018-06-24T00:00:00Z	1129407	35562	Conda
        bedtools==2.27.0--he941832_2	2018-06-24T00:00:00Z	1129407	35562	Conda
        bedtools==2.27.0--he513fc3_4	2018-06-24T00:00:00Z	1129407	35562	Conda
        quay.io/biocontainers/bedtools:2.27.0--1	2018-02-14T00:00:00Z	14094467	0	Docker
        quay.io/biocontainers/bedtools:2.27.0--0	2017-12-07T00:00:00Z	14087205	0	Docker
        ```
        
        #### Get latest docker image for bedtools version 2.27.0
        
        ```bash
        > bioconda2biocontainer --package_name bedtools --package_version 2.27.0 --container_type Docker
        quay.io/biocontainers/bedtools:2.27.0--he513fc3_4
        ```
        
        #### Get smaller singularity image for bedtools version 2.27.0
        
        ```bash
        > bioconda2biocontainer --package_name bedtools --package_version 2.27.0 --container_type Singularity --sort_by_size
        https://depot.galaxyproject.org/singularity/bedtools:2.27.0--he860b03_3
        ```
        
        #### Get the conda package with more downloads for bedtools version 2.27.0
        
        ```bash
        > bioconda2biocontainer --package_name bedtools --package_version 2.27.0 --container_type Conda --sort_by_download
        bedtools==2.27.0--he860b03_3
        ```
        
        #### 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
        ```
        
        ### biocontainers-search
        
        Search tools in Biocontainers registry and return a TAB separated table with Name, Versions (comma separated),
        Description, License and number of pulls. 
        
        #### Search proteomics tools
        
        ```bash
        > biocontainers-search --search_term proteomics
        name	versions	description	license	pulls
        augustus	v3.3.2dfsg-2-deb,v3.2.3dfsg-1-deb,3.3.3,3.3.2,3.3,3.2.3,3.2.2,3.1	Augustus is a eukaryotic gene prediction tool. it can integrate evidence, e.g. from rna-seq, ests, proteomics, but can also predict genes ab initio. the ppx extension to augustus can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. it can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.	Artistic-1.0	448371
        bioconductor-assessorf	1.6.0,1.4.0,1.2.0,1.0.2	Assess Gene Predictions Using Proteomics and Evolutionary Conservation	GPL-3	915
        bioconductor-customprodb	1.28.0,1.26.0,1.24.0,1.22.0,1.14.0	Generate customized protein database from ngs data, with a focus on rna-seq data, for proteomics search	Not available	10520
        ```
        
        #### Search proteomics tools and return JSON data
        
        ```bash
        > biocontainers-search --search_term proteomics --json
        [
            {
                "contains": [],
                "description": "Augustus is a eukaryotic gene prediction tool. it can integrate evidence, e.g. from rna-seq, ests, proteomics, but can also predict genes ab initio. the ppx extension to augustus can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. it can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.",
                "id": "augustus",
                "identifiers": [
                    "biotools:augustus",
                    "PMID:15215400"
                ],
                "license": "Artistic-1.0",
                "name": "augustus",
                "organization": "biocontainers",
                "pulls": 448371,
                "tool_tags": [
                    "biology",
                    "bioinformatics",
                    "c++",
                    "commandline",
                    "program",
                    "calculation",
                    "utility",
                    "ncurses",
                    "analysing",
                    "biological-sequence"
                ],
                "tool_url": "https://github.com/Gaius-Augustus/Augustus",
                "toolclass": {
                    "description": "CommandLineTool",
                    "id": "0",
                    "name": "CommandLineTool"
                },
                "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/augustus",
                "versions": [
                    {
                        "id": "augustus-3.2.3",
                        "meta_version": "3.2.3",
                        "name": "augustus",
                        "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/augustus/versions/augustus-3.2.3"
                    },
                    {
                        "id": "augustus-3.2.2",
                        "meta_version": "3.2.2",
                        "name": "augustus",
                        "url": "http://api.biocontainers.pro/ga4gh/trs/v2/tools/augustus/versions/augustus-3.2.2"
                    },
                    ...
        ```
        
        ### bioconda2cwldocker
        
        This script reads a conda env yaml file and replace, for each package in the environment, the images defined 
        in the CWL or Yaml files inside the directory pass in the option **cwl_path**
        
        #### Example
        
        We would like to use the CWLs defined in the repo https://github.com/ncbi/cwl-ngs-workflows-cbb with the versions 
        defined in this conda env:
        
        ###### Conda env file
        
        ```yaml
        name: rnaseq
        channels:
          - conda-forge
          - bioconda
          - defaults
        dependencies:
          - bedtools=2.29.2
          - fastqc=0.11.9
          - sra-tools=2.10.8
          - star=2.7.5a
        ```
        
        ###### Cloning the repo
        
        ```bash
        $ git clone https://github.com/ncbi/cwl-ngs-workflows-cbb
        Cloning into 'cwl-ngs-workflows-cbb'...
        remote: Enumerating objects: 94, done.
        remote: Counting objects: 100% (94/94), done.
        remote: Compressing objects: 100% (69/69), done.
        remote: Total 1924 (delta 47), reused 50 (delta 25), pack-reused 1830
        Receiving objects: 100% (1924/1924), 319.82 KiB | 3.48 MiB/s, done.
        Resolving deltas: 100% (1216/1216), done.
        ```
        
        ###### Print defined images for the tools in the CWLs
        
        ```bash
        $ cat cwl-ngs-workflows-cbb/tools/bedtools/bedtools.yml
         class: DockerRequirement
         dockerPull: quay.io/biocontainers/bedtools:2.28.0--hdf88d34_0
        
        $ cat cwl-ngs-workflows-cbb/tools/fastqc/fastqc.yml
         class: DockerRequirement
         dockerPull: quay.io/biocontainers/fastqc:0.11.8--1
        
        $ cat cwl-ngs-workflows-cbb/tools/sra-toolkit/sra-toolkit.yml
         class: DockerRequirement
         dockerPull: quay.io/biocontainers/sra-tools:2.10.7--pl526haddd2b5_1
        
        $ cat cwl-ngs-workflows-cbb/tools/star/star.yml
         class: DockerRequirement
         dockerPull: quay.io/biocontainers/star:2.7.5a--0
        ```
        
        ###### Running bioconda2cwldocker
        
        ```bash
        $ bioconda2cwldocker --conda_env_file conda-env.yaml --cwl_path cwl-ngs-workflows-cbb/
        bedtools with version 2.29.2 update image to: quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0
        	cwl-ngs-workflows-cbb/tools/bedtools/bedtools.yml with old image replaced: quay.io/biocontainers/bedtools:2.28.0--hdf88d34_0
        fastqc with version 0.11.9 update image to: quay.io/biocontainers/fastqc:0.11.9--0
        	cwl-ngs-workflows-cbb/tools/fastqc/fastqc.yml with old image replaced: quay.io/biocontainers/fastqc:0.11.8--1
        sra-tools with version 2.10.8 update image to: quay.io/biocontainers/sra-tools:2.10.8--pl526haddd2b5_0
        	cwl-ngs-workflows-cbb/tools/sra-toolkit/sra-toolkit.yml with old image replaced: quay.io/biocontainers/sra-tools:2.10.7--pl526haddd2b5_1
        ```
        
        ##### Print new defined images for the tools in the CWLs
        
        ```bash
        $ cat cwl-ngs-workflows-cbb/tools/bedtools/bedtools.yml
         class: DockerRequirement
         dockerPull: quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0
        
        $ cat cwl-ngs-workflows-cbb/tools/fastqc/fastqc.yml
         class: DockerRequirement
         dockerPull: quay.io/biocontainers/fastqc:0.11.9--0
        
        $ cat cwl-ngs-workflows-cbb/tools/sra-toolkit/sra-toolkit.yml
         class: DockerRequirement
         dockerPull: quay.io/biocontainers/sra-tools:2.10.8--pl526haddd2b5_0
        
        $ cat cwl-ngs-workflows-cbb/tools/star/star.yml
         class: DockerRequirement
         dockerPull: quay.io/biocontainers/star:2.7.5a--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
