Find biocontainer images for tools
Project description
bioconda2biocontainer
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"
},
...
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"
}
]
}
>>>
Project details
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Hashes for bioconda2biocontainer-0.0.2.tar.gz
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Hashes for bioconda2biocontainer-0.0.2-py3-none-any.whl
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