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bioconda2biocontainer

Python package

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

> 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

> 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

> 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

> 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

> 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

> 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

> 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 passed 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
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
$ 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
$ 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
$ 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
$ 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

Note that the STAR image name was not changed as the CWL was using the same version

Install

pip install bioconda2biocontainer

For development:

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:

py.test

API

Demo

>>> 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"
        }
    ]
}
>>>

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