bioblend

A Python library for interacting with the Galaxy API

https://github.com/galaxyproject/bioblend

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
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Academic publication links
✓
Committers with academic emails
8 of 65 committers (12.3%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (5.2%) to scientific vocabulary

Keywords

api api-client cloudman hacktoberfest usegalaxy

Keywords from Contributors

bioinformatics genomics cwl english lesson next-generation-sequencing bioinformatics-pipeline parallel-computing workflow-engine

Last synced: 6 months ago · JSON representation ·

Repository

A Python library for interacting with the Galaxy API

Basic Info

Host: GitHub
Owner: galaxyproject
License: mit
Language: Python
Default Branch: main
Homepage: https://bioblend.readthedocs.io/
Size: 17 MB

Statistics

Stars: 93
Watchers: 28
Forks: 121
Open Issues: 35
Releases: 17

Topics

api api-client cloudman hacktoberfest usegalaxy

Created over 13 years ago · Last pushed 7 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation

README.rst

.. image:: https://img.shields.io/pypi/v/bioblend.svg
    :target: https://pypi.org/project/bioblend/
    :alt: latest version available on PyPI

.. image:: https://readthedocs.org/projects/bioblend/badge/
    :alt: Documentation Status
    :target: https://bioblend.readthedocs.io/

.. image:: https://badges.gitter.im/galaxyproject/bioblend.svg
   :alt: Join the chat at https://gitter.im/galaxyproject/bioblend
   :target: https://gitter.im/galaxyproject/bioblend?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge


BioBlend is a Python library for interacting with the `Galaxy`_ API.

BioBlend is supported and tested on:

- Python 3.9 - 3.14
- Galaxy release 19.05 and later.

Full docs are available at https://bioblend.readthedocs.io/ with a quick library
overview also available in `ABOUT.rst <./ABOUT.rst>`_.

.. References/hyperlinks used above
.. _Galaxy: https://galaxyproject.org/

Owner

Name: Galaxy Project
Login: galaxyproject
Kind: organization
Email: outreach@galaxyproject.org

Website: http://galaxyproject.org/
Repositories: 133
Profile: https://github.com/galaxyproject

Galaxy is an open, web-based platform for data-intensive research.

Citation (CITATION)

If you use BioBlend in your published work, please cite the following article:

- Clare Sloggett, Nuwan Goonasekera, Enis Afgan "BioBlend: automating pipeline
  analyses within Galaxy and CloudMan"
  Bioinformatics (2013) 29(13):1685-1686 doi:10.1093/bioinformatics/btt199

BibTeX format:

@article{10.1093/bioinformatics/btt199,
  author = {Sloggett, Clare and Goonasekera, Nuwan and Afgan, Enis},
  doi = {10.1093/bioinformatics/btt199},
  journal = {Bioinformatics},
  number = {13},
  pages = {1685-1686},
  title = {{BioBlend: automating pipeline analyses within Galaxy and CloudMan}},
  url = {https://doi.org/10.1093/bioinformatics/btt199},
  volume = {29},
  year = {2013},
}

If you use BioBlend.objects in your published work, please cite the following
article:

- Simone Leo, Luca Pireddu, Gianmauro Cuccuru, Luca Lianas, Nicola Soranzo, Enis
  Afgan, Gianluigi Zanetti "BioBlend.objects: metacomputing with Galaxy"
  Bioinformatics (2014) 30(19):2816-2817 doi:10.1093/bioinformatics/btu386

BibTeX format:

@article{10.1093/bioinformatics/btu386,
  author = {Leo, Simone and Pireddu, Luca and Cuccuru, Gianmauro and Lianas, Luca and Soranzo, Nicola and Afgan, Enis and Zanetti, Gianluigi},
  doi = {10.1093/bioinformatics/btu386},
  journal = {Bioinformatics},
  number = {19},
  pages = {2816-2817},
  title = {{BioBlend.objects: metacomputing with Galaxy}},
  url = {https://doi.org/10.1093/bioinformatics/btu386},
  volume = {30},
  year = {2014},
}

GitHub Events

Total

Create event: 1
Release event: 2
Issues event: 8
Watch event: 6
Issue comment event: 29
Push event: 19
Pull request event: 25
Pull request review comment event: 49
Pull request review event: 44
Fork event: 6

Last Year

Create event: 1
Release event: 2
Issues event: 8
Watch event: 6
Issue comment event: 29
Push event: 19
Pull request event: 25
Pull request review comment event: 49
Pull request review event: 44
Fork event: 6

Committers

Last synced: 9 months ago

All Time

Total Commits: 1,857
Total Committers: 65
Avg Commits per committer: 28.569
Development Distribution Score (DDS): 0.673

Past Year

Commits: 47
Committers: 8
Avg Commits per committer: 5.875
Development Distribution Score (DDS): 0.532

Top Committers

Name	Email	Commits
Nicola Soranzo	n**o@e**k	608
rikeshi	r****i	235
Enis Afgan	a**e@g**m	149
simleo	s**o@c**t	142
Simon Bray	s**1@g**m	106
John Chilton	j**n@g**m	54
cat-bro	c**b@g**m	50
Eric Rasche	r**c@g**m	50
Nuwan Goonasekera	n**g@g**m	47
Anthony Bretaudeau	a**u@i**r	35
Philip Mabon	p**n@g**m	32
Fabio Cumbo	f**o@g**m	31
mvdbeek	m**k@g**m	26
Matthias Bernt	m**t@u**e	24
Gregory Long	g**g@g**m	22
Luca Pireddu	p**u@c**t	19
Marco Enrico Piras	k**p@c**t	17
Joshi	j**j@l**t	17
Dannon Baker	d**r@m**m	16
Alex MacLean	m**9@g**m	14
Eric Rasche	r**c@y**u	12
Martin Cech	c**n@g**m	10
abretaud	a**u@r**r	9
Fred	f**t@l**m	9
David Christiany	3****y	9
Nathan Edwards	e****j	9
Clare Sloggett	c**t@g**m	8
ashvark	a**k@g**m	6
Oleg Zharkov	o**2@g**m	6
Gianmauro Cuccuru	g**o@c**t	6
and 35 more...

Committer Domains (Top 20 + Academic)

crs4.it: 5 earlham.ac.uk: 1 inria.fr: 1 ufz.de: 1 lri-108042.lerner.ad.cchs.net: 1 me.com: 1 yandex.ru: 1 rennes.inra.fr: 1 limagrain.com: 1 i2labs.ca: 1 bx.psu.edu: 1 uno.edu: 1 50mail.com: 1 scilifelab.se: 1 gruenings.eu: 1 emory.edu: 1 inra.fr: 1 psu.edu: 1 andreas-sk.de: 1 gitter.im: 1 pasteur.fr: 1 latrobe.edu.au: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 34
Total pull requests: 121
Average time to close issues: almost 2 years
Average time to close pull requests: 3 months
Total issue authors: 27
Total pull request authors: 31
Average comments per issue: 2.97
Average comments per pull request: 1.4
Merged pull requests: 98
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 3
Pull requests: 28
Average time to close issues: 1 day
Average time to close pull requests: 15 days
Issue authors: 3
Pull request authors: 8
Average comments per issue: 1.67
Average comments per pull request: 1.0
Merged pull requests: 19
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

simonbray (5)
nsoranzo (3)
innovate-invent (2)
anilthanki (1)
Paprikant (1)
chambm (1)
pjbriggs (1)
hexylena (1)
liuyaguo (1)
deepsidhu85 (1)
heisner-tillman (1)
lstrgar (1)
gallardoalba (1)
hehao98 (1)
mvdbeek (1)

Pull Request Authors

bernt-matthias (20)
simonbray (14)
cumbof (12)
mvdbeek (10)
jaidevjoshi83 (10)
cat-bro (9)
Smeds (8)
nsoranzo (8)
rikeshi (6)
dannon (3)
hexylena (3)
thepineapplepirate (3)
minhtrung1997 (2)
ahmedhamidawan (2)
jdavcs (2)

Top Labels

Issue Labels

enhancement (4) paper-cut (3) documentation (2)

Pull Request Labels

enhancement (2)

Packages

Total packages: 1
Total downloads:
- pypi 266,052 last-month
Total docker downloads: 4,521

Total dependent packages: 13
Total dependent repositories: 133
Total versions: 38
Total maintainers: 3

pypi.org: bioblend

Library for interacting with the Galaxy API

Homepage: https://bioblend.readthedocs.io/
Documentation: https://bioblend.readthedocs.io/
License: MIT
Latest release: 1.6.0
published 8 months ago

Versions: 38
Dependent Packages: 13
Dependent Repositories: 133
Downloads: 266,052 Last month
Docker Downloads: 4,521

Rankings

Dependent packages count: 0.9%

Dependent repos count: 1.3%

Docker downloads count: 1.4%

Downloads: 1.6%

Average: 2.9%

Forks count: 4.4%

Stargazers count: 7.6%

Maintainers (3)

mvdbeek nsoranzo afgane

Last synced: 6 months ago

Dependencies

docs/requirements.txt pypi

sphinx >=2
sphinx-rtd-theme *

.github/workflows/deploy.yaml actions

actions/checkout v3 composite
actions/setup-python v4 composite
pypa/gh-action-pypi-publish release/v1 composite

.github/workflows/lint.yaml actions

actions/checkout v3 composite
actions/setup-python v4 composite

.github/workflows/test.yaml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/setup-python v4 composite
postgres 11 docker

pyproject.toml pypi

setup.py pypi