Find biocontainer images for Bioconda packages
Project 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
> 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
> 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
> 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
> 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
> 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
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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Close
Hashes for bioconda2biocontainer-0.0.1.tar.gz
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 4f01ed9a366743aa4ed497bf26a74bbe2bd2cbcf8a76952fbd08014f14aab12e |
|
| MD5 | e39b587a39cdc204ada3d32f702d01bd |
|
| BLAKE2b-256 | 6c95d6d5dcb87a245f05155e471cd6f8367dd0d31fcc34dded3d0d53624864e3 |
Close
Hashes for bioconda2biocontainer-0.0.1-py3-none-any.whl
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | ba7bdb0b255aa7a5d764f4fdef0c9683edd5406e0a0095b6f819297f3adcf279 |
|
| MD5 | c416ba8d0815cd606c1900eb685e91b9 |
|
| BLAKE2b-256 | 7e4c490b7ce97505c5dc6d9be7eb6e8538c6903f5ea61c69f9c84db27fcd3c66 |
