galaxy

Data intensive science for everyone.

https://github.com/galaxyproject/galaxy

Science Score: 36.0%

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

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
○
Academic publication links
✓
Committers with academic emails
122 of 471 committers (25.9%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (11.7%) to scientific vocabulary

Keywords

bioinformatics dna genomics hacktoberfest ngs pipeline science sequencing usegalaxy workflow workflow-engine

Keywords from Contributors

cloudman cwl workflows lesson common-workflow-language novice english beta nf-core nextflow

Last synced: 6 months ago · JSON representation

Repository

Data intensive science for everyone.

Basic Info

Host: GitHub
Owner: galaxyproject
License: other
Language: Python
Default Branch: dev
Homepage: https://galaxyproject.org
Size: 662 MB

Statistics

Stars: 1,593
Watchers: 69
Forks: 1,075
Open Issues: 2,552
Releases: 30

Topics

bioinformatics dna genomics hacktoberfest ngs pipeline science sequencing usegalaxy workflow workflow-engine

Created almost 11 years ago · Last pushed 6 months ago

Metadata Files

Readme Contributing License Code of conduct Citation Security

README.rst

.. figure:: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo.jpg
   :alt: Galaxy Logo

The latest information about Galaxy can be found on the `Galaxy Community Hub `__.

Community support is available at `Galaxy Help `__.

.. image:: https://img.shields.io/badge/chat-gitter-blue.svg
    :target: https://gitter.im/galaxyproject/Lobby
    :alt: Chat on gitter

.. image:: https://img.shields.io/badge/chat-irc.freenode.net%23galaxyproject-blue.svg
    :target: https://webchat.freenode.net/?channels=galaxyproject
    :alt: Chat on irc

.. image:: https://img.shields.io/badge/release-documentation-blue.svg
    :target: https://docs.galaxyproject.org/en/master/
    :alt: Release Documentation

.. image:: https://travis-ci.org/galaxyproject/galaxy.svg?branch=dev
    :target: https://travis-ci.org/galaxyproject/galaxy
    :alt: Inspect the test results

Galaxy Quickstart
=================

Galaxy requires Python 3.9 or higher. To check your Python version, run:

.. code:: console

    $ python -V
    Python 3.9.21

Start Galaxy:

.. code:: console

    $ sh run.sh

Once Galaxy completes startup, you should be able to view Galaxy in your
browser at: http://localhost:8080

For more installation details please see: https://getgalaxy.org/

Documentation is available at: https://docs.galaxyproject.org/

Tutorials on how to use Galaxy, perform scientific analyses with it, develop Galaxy and its tools, and admin a Galaxy server are at: https://training.galaxyproject.org/

Tools
=====

Tools can be either installed from the Tool Shed or added manually.
For details please see the `tutorial `__.
Note that not all dependencies for the tools provided in the
``tool_conf.xml.sample`` are included. To install them please visit
"Manage dependencies" in the admin interface.

Issues and Galaxy Development
=============================

Please see `CONTRIBUTING.md `_ .

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.

Committers

Last synced: 9 months ago

All Time

Total Commits: 65,700
Total Committers: 471
Avg Commits per committer: 139.49
Development Distribution Score (DDS): 0.875

Past Year

Commits: 5,572
Committers: 67
Avg Commits per committer: 83.164
Development Distribution Score (DDS): 0.867

Top Committers

Name	Email	Commits
guerler	a**r@g**m	8,214
John Chilton	j**n@g**m	6,674
mvdbeek	m**k@g**m	6,509
Dannon Baker	d**r@g**m	6,063
davelopez	4****z	2,837
John Davis	j**s@g**m	2,828
Greg Von Kuster	g**g@b**u	2,324
Nicola Soranzo	n**o@e**k	2,250
Nate Coraor	n**e@b**u	2,095
Daniel Blankenberg	d**n@b**u	1,780
Martin Cech	m**n@b**u	1,518
Jeremy Goecks	j**s@e**u	1,514
Matthias Bernt	m**t@u**e	1,454
Laila Los	4****y	1,352
Carl Eberhard	c**d@g**m	1,254
Alireza Heidari	i**h@g**m	984
Dave Bouvier	d**e@b**u	977
Ahmed Awan	q**3@u**u	797
James Taylor	j**s@j**g	780
Oleg Zharkov	o**2@g**m	765
Bjoern Gruening	b**g@g**m	739
Helena Rasche	h**r@h**g	679
vahid	j**d@g**m	627
Assunta DeSanto	a**3@g**m	466
anuprulez	a**z@g**m	425
Kanwei Li	k**i@g**m	380
Tillman	t**r@p**e	359
Nuwan Goonasekera	2****g	285
Ramkrishna Chakrabarty	rc@b****u	267
Mason	n**n@g**m	250
and 441 more...

Committer Domains (Top 20 + Academic)

bx.psu.edu: 22 informatik.uni-freiburg.de: 5 umn.edu: 5 pasteur.fr: 4 iu.edu: 4 uncc.edu: 4 emory.edu: 3 jhu.edu: 3 localhost.localdomain: 3 lumc.nl: 3 unimelb.edu.au: 2 crs4.it: 2 psb.ugent.be: 2 utsouthwestern.edu: 2 nbic.nl: 2 temple.edu: 2 uio.no: 2 msi.umn.edu: 2 irisa.fr: 2 apache.org: 2 manchester.ac.uk: 2 ornl.gov: 2 epfl.ch: 2 inria.fr: 2 gwu.edu: 2 stfc.ac.uk: 1 cs.wisc.edu: 1 tufts.edu: 1 cs.uni-freiburg.de: 1 geo.uio.no: 1 uno.edu: 1 ucsc.edu: 1 uct.ac.za: 1 bu.edu: 1 tf.uni-freiburg.de: 1 lhup.edu: 1 infra04-wg396.visitor.eduroam.wireless.umn.edu: 1 sanbi.ac.za: 1 psu.edu: 1 umbc.edu: 1 earlham.ac.uk: 1 gsb.columbia.edu”: 1 princeton.edu: 1 gatech.edu: 1 biologie.uni-freiburg.de: 1 nau.edu: 1 uni-koeln.de: 1 uwaterloo.ca: 1 uni-rostock.de: 1 p-body.win.ad.jhu.edu: 1 uga.edu: 1 usit.uio.no: 1 udo.edu: 1 ntnu.no: 1 uconn.edu: 1 alum.mit.edu: 1 vbi.vt.edu: 1 latrobe.edu.au: 1 email.arizona.edu: 1 uci.edu: 1 ncbi.nlm.nih.gov: 1 ebi.ac.uk: 1 uni-due.de: 1 galaxyc.win.ad.jhu.edu: 1 oregonstate.edu: 1 tamu.edu: 1 ubuntu-base.localdomain: 1 informatik.uni-leipzig.de: 1 louisville.edu: 1 sn04.bi.uni-freiburg.de: 1 soe.ucsc.edu: 1 imtek.uni-freiburg.de: 1 mq.edu.au: 1 rc.ufl.edu: 1 epcc.ed.ac.uk: 1 nd.edu: 1 mit.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 1,767
Total pull requests: 4,829
Average time to close issues: 9 months
Average time to close pull requests: 29 days
Total issue authors: 192
Total pull request authors: 148
Average comments per issue: 1.7
Average comments per pull request: 1.57
Merged pull requests: 3,524
Bot issues: 120
Bot pull requests: 108

Past Year

Issues: 702
Pull requests: 2,217
Average time to close issues: 12 days
Average time to close pull requests: 9 days
Issue authors: 99
Pull request authors: 68
Average comments per issue: 0.9
Average comments per pull request: 1.27
Merged pull requests: 1,552
Bot issues: 66
Bot pull requests: 71

View more stats

Top Authors

Issue Authors

mvdbeek (252)
martenson (137)
galaxyproject-sentryintegration[bot] (120)
hexylena (116)
bernt-matthias (112)
jmchilton (80)
ahmedhamidawan (68)
bgruening (61)
davelopez (47)
jennaj (47)
Delphine-L (36)
guerler (32)
jdavcs (29)
wm75 (27)
dannon (26)

Pull Request Authors

mvdbeek (952)
jmchilton (507)
davelopez (401)
ahmedhamidawan (311)
guerler (284)
jdavcs (280)
nsoranzo (267)
bernt-matthias (253)
dannon (236)
ElectronicBlueberry (141)
galaxybot (117)
itisAliRH (116)
dependabot[bot] (108)
martenson (99)
natefoo (79)

Top Labels

Issue Labels

kind/bug (668) area/UI-UX (572) area/backend (163) area/workflows (159) kind/enhancement (147) feature-request (123) area/API (85) release-testing-24.0 (47) help wanted (45) area/database (41) paper-cut (38) kind/feature (35) area/jobs (34) area/tools (30) area/toolshed (29) area/dataset-collections (26) area/admin (26) planning (25) area/performance (21) area/testing (21) area/visualizations (19) kind/refactoring (17) area/objectstore (17) area/tool-framework (16) area/documentation (16) status/planning (16) area/histories (15) release-testing-25.0 (15) area/auth (13) release-testing-24.1 (13)

Pull Request Labels

kind/bug (2,272) area/UI-UX (1,455) kind/enhancement (1,198) area/testing (580) area/tool-framework (525) area/API (498) kind/refactoring (454) area/database (369) area/workflows (366) area/dependencies (274) area/datatypes (244) area/jobs (242) area/backend (207) kind/feature (198) area/documentation (194) area/client (192) area/visualizations (165) area/admin (151) minor (146) area/testing/integration (139) area/testing/api (133) area/packaging (128) area/tools (122) area/objectstore (121) merge (120) dependencies (120) area/util (99) area/tool-dependencies (96) area/auth (93) area/testing/selenium (91)

Packages

Total packages: 41
Total downloads:
- pypi 81,110 last-month
- npm 798 last-month
Total docker downloads: 81,162

Total dependent packages: 110
(may contain duplicates)
Total dependent repositories: 206
(may contain duplicates)
Total versions: 775
Total maintainers: 7
Total advisories: 1

pypi.org: galaxy-tool-util

Galaxy tool and tool dependency utilities

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-tool-util.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 74
Dependent Packages: 16
Dependent Repositories: 43
Downloads: 22,082 Last month
Docker Downloads: 27,048

Rankings

Dependent packages count: 0.9%

Forks count: 1.3%

Docker downloads count: 1.4%

Average: 1.6%

Stargazers count: 1.9%

Downloads: 2.0%

Dependent repos count: 2.2%

Maintainers (3)

jmchilton mvdbeek natefoo

Last synced: 6 months ago

pypi.org: galaxy-util

Galaxy generic utilities

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-util.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 49
Dependent Packages: 23
Dependent Repositories: 23
Downloads: 27,886 Last month
Docker Downloads: 27,048

Rankings

Forks count: 1.3%

Docker downloads count: 1.4%

Dependent packages count: 1.6%

Average: 1.9%

Stargazers count: 1.9%

Downloads: 2.0%

Dependent repos count: 3.1%

Maintainers (3)

jmchilton mvdbeek natefoo

Last synced: 6 months ago

pypi.org: galaxy-containers

Galaxy Container Modeling and Interaction Abstractions

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-containers.readthedocs.io/
License: AFL
Latest release: 22.1.1
published over 3 years ago

Versions: 6
Dependent Packages: 4
Dependent Repositories: 13
Downloads: 1,546 Last month
Docker Downloads: 27,048

Rankings

Forks count: 1.3%

Docker downloads count: 1.4%

Stargazers count: 1.9%

Dependent packages count: 2.2%

Average: 3.1%

Dependent repos count: 4.1%

Downloads: 7.6%

Maintainers (2)

jmchilton mvdbeek

Last synced: 6 months ago

pypi.org: galaxy-objectstore

Galaxy objectstore framework and plugins

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-objectstore.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 38
Dependent Packages: 5
Dependent Repositories: 13
Downloads: 982 Last month

Rankings

Forks count: 1.3%

Stargazers count: 1.9%

Dependent packages count: 3.3%

Average: 3.6%

Dependent repos count: 4.1%

Downloads: 7.4%

Maintainers (2)

jmchilton mvdbeek

Last synced: 6 months ago

pypi.org: galaxy-job-metrics

Galaxy job metrics

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-job-metrics.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 35
Dependent Packages: 3
Dependent Repositories: 10
Downloads: 744 Last month

Rankings

Forks count: 1.3%

Stargazers count: 1.9%

Dependent packages count: 3.3%

Average: 3.8%

Dependent repos count: 4.7%

Downloads: 7.6%

Maintainers (2)

jmchilton mvdbeek

Last synced: 6 months ago

pypi.org: galaxy-job-execution

Galaxy job execution runtime utilities

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-job-execution.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 33
Dependent Packages: 5
Dependent Repositories: 10
Downloads: 601 Last month

Rankings

Forks count: 1.3%

Stargazers count: 1.9%

Dependent packages count: 2.2%

Average: 4.1%

Dependent repos count: 4.7%

Downloads: 10.3%

Maintainers (2)

jmchilton mvdbeek

Last synced: 6 months ago

pypi.org: galaxy-app

Galaxy application (backend)

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-app.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 32
Dependent Packages: 4
Dependent Repositories: 13
Downloads: 571 Last month

Rankings

Forks count: 1.3%

Stargazers count: 1.9%

Dependent packages count: 3.3%

Dependent repos count: 4.1%

Average: 4.4%

Downloads: 11.3%

Maintainers (3)

jmchilton mvdbeek natefoo

Advisories (1)

Galaxy cross-site scripting (XSS)

Last synced: 6 months ago

pypi.org: galaxy-data

Galaxy datatype framework and datatypes

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-data.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 37
Dependent Packages: 9
Dependent Repositories: 13
Downloads: 878 Last month

Rankings

Forks count: 1.3%

Stargazers count: 1.9%

Dependent repos count: 4.1%

Average: 4.9%

Dependent packages count: 7.4%

Downloads: 9.7%

Maintainers (3)

jmchilton mvdbeek jdavcs

Last synced: 6 months ago

spack.io: py-galaxy-util

Galaxy Generic Utilities

Homepage: https://github.com/galaxyproject/galaxy
License: []
Latest release: 22.1.2
published about 3 years ago

Versions: 1
Dependent Packages: 5
Dependent Repositories: 0

Rankings

Dependent repos count: 0.0%

Forks count: 3.1%

Average: 5.1%

Stargazers count: 7.4%

Dependent packages count: 9.7%

Maintainers (1)

adamjstewart

Last synced: 6 months ago

pypi.org: galaxy-web-stack

Galaxy web stack abstraction

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-web-stack.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 31
Dependent Packages: 5
Dependent Repositories: 10
Downloads: 620 Last month

Rankings

Forks count: 1.3%

Stargazers count: 1.9%

Dependent repos count: 4.7%

Average: 5.1%

Dependent packages count: 7.4%

Downloads: 10.4%

Maintainers (2)

jmchilton mvdbeek

Last synced: 6 months ago

pypi.org: galaxy-web-framework

Galaxy web framework

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-web-framework.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 32
Dependent Packages: 4
Dependent Repositories: 10
Downloads: 633 Last month

Rankings

Forks count: 1.3%

Stargazers count: 1.9%

Dependent repos count: 4.7%

Average: 5.1%

Dependent packages count: 7.4%

Downloads: 10.4%

Maintainers (2)

jmchilton mvdbeek

Last synced: 6 months ago

pypi.org: galaxy-auth

Galaxy auth framework and implementations

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-auth.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 32
Dependent Packages: 2
Dependent Repositories: 10
Downloads: 565 Last month

Rankings

Forks count: 1.3%

Stargazers count: 1.9%

Dependent repos count: 4.7%

Average: 5.2%

Dependent packages count: 7.4%

Downloads: 10.5%

Maintainers (2)

jmchilton mvdbeek

Last synced: 6 months ago

pypi.org: galaxy-files

Galaxy file source framework and default plugins

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-files.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 29
Dependent Packages: 4
Dependent Repositories: 6
Downloads: 763 Last month

Rankings

Forks count: 1.3%

Stargazers count: 1.9%

Average: 5.4%

Dependent repos count: 6.1%

Dependent packages count: 7.4%

Downloads: 10.1%

Maintainers (2)

jmchilton mvdbeek

Last synced: 6 months ago

pypi.org: galaxy-config

Galaxy configuration

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-config.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 29
Dependent Packages: 3
Dependent Repositories: 3
Downloads: 535 Last month

Rankings

Forks count: 1.3%

Stargazers count: 1.9%

Average: 6.1%

Dependent packages count: 7.4%

Dependent repos count: 9.2%

Downloads: 10.5%

Maintainers (2)

jmchilton mvdbeek

Last synced: 6 months ago

pypi.org: galaxy-test-base

Galaxy testing utilities

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-test-base.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 31
Dependent Packages: 2
Dependent Repositories: 9
Downloads: 398 Last month

Rankings

Forks count: 1.3%

Stargazers count: 1.9%

Dependent packages count: 3.3%

Dependent repos count: 5.0%

Average: 6.1%

Downloads: 18.9%

Maintainers (2)

jmchilton mvdbeek

Last synced: 6 months ago

pypi.org: galaxy

Galaxy server metapackage

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 3
Downloads: 164 Last month
Docker Downloads: 0

Rankings

Docker downloads count: 1.0%

Average: 6.7%

Dependent repos count: 9.0%

Dependent packages count: 10.0%

Maintainers (2)

jmchilton mvdbeek

Last synced: 6 months ago

proxy.golang.org: github.com/galaxyproject/galaxy

Documentation: https://pkg.go.dev/github.com/galaxyproject/galaxy#section-documentation
License: other
Latest release: v25.0.2+incompatible
published 6 months ago

Versions: 34
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 6.5%

Average: 6.7%

Dependent repos count: 6.9%

Last synced: 6 months ago

npmjs.org: @galaxyproject/galaxy-client

Galaxy client application build system

Homepage: https://github.com/galaxyproject/galaxy#readme
License: MIT
Latest release: 24.2.4
published 8 months ago

Versions: 6
Dependent Packages: 2
Dependent Repositories: 9
Downloads: 798 Last month
Docker Downloads: 18

Rankings

Forks count: 1.3%

Stargazers count: 2.4%

Dependent repos count: 4.0%

Average: 7.2%

Dependent packages count: 8.8%

Downloads: 19.4%

Maintainers (4)

jmchilton mvdbeek dannon guerler

Last synced: 6 months ago

spack.io: py-galaxy-tool-util

The Galaxy tool utilities.

Homepage: https://github.com/galaxyproject/galaxy
License: []
Latest release: 22.1.5
published about 3 years ago

Versions: 1
Dependent Packages: 2
Dependent Repositories: 0

Rankings

Dependent repos count: 0.0%

Forks count: 3.1%

Average: 7.4%

Stargazers count: 7.4%

Dependent packages count: 19.0%

Maintainers (1)

adamjstewart

Last synced: 6 months ago

spack.io: py-galaxy-objectstore

The Galaxy object store framework and default implementations.

Homepage: https://github.com/galaxyproject/galaxy
License: []
Latest release: 22.1.1
published about 3 years ago

Versions: 1
Dependent Packages: 1
Dependent Repositories: 0

Rankings

Dependent repos count: 0.0%

Forks count: 3.1%

Stargazers count: 7.4%

Average: 9.6%

Dependent packages count: 28.1%

Maintainers (1)

adamjstewart

Last synced: 6 months ago

spack.io: py-galaxy-job-metrics

The Galaxy job metrics framework and default plugins.

Homepage: https://github.com/galaxyproject/galaxy
License: []
Latest release: 22.1.1
published about 3 years ago

Versions: 1
Dependent Packages: 1
Dependent Repositories: 0

Rankings

Dependent repos count: 0.0%

Forks count: 3.1%

Stargazers count: 7.4%

Average: 9.6%

Dependent packages count: 28.1%

Maintainers (1)

adamjstewart

Last synced: 6 months ago

spack.io: py-galaxy-containers

The Galaxy containers module - interfaces for modeling and interacting with container backends (docker and docker swarm currently).

Homepage: https://github.com/galaxyproject/galaxy
License: []
Latest release: 22.1.1
published about 3 years ago

Versions: 1
Dependent Packages: 1
Dependent Repositories: 0

Rankings

Dependent repos count: 0.0%

Forks count: 3.1%

Stargazers count: 7.4%

Average: 9.6%

Dependent packages count: 28.1%

Maintainers (1)

adamjstewart

Last synced: 6 months ago

pypi.org: galaxy-test-driver

Galaxy test driver

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-test-driver.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 31
Dependent Packages: 1
Dependent Repositories: 1
Downloads: 322 Last month

Rankings

Forks count: 1.3%

Stargazers count: 1.9%

Dependent packages count: 3.3%

Average: 10.3%

Dependent repos count: 22.2%

Downloads: 22.7%

Maintainers (2)

jmchilton mvdbeek

Last synced: 6 months ago

pypi.org: galaxy-selenium

Galaxy Selenium interaction framework

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-selenium.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 32
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 309 Last month

Rankings

Forks count: 1.3%

Stargazers count: 1.9%

Dependent packages count: 7.4%

Average: 10.6%

Downloads: 20.4%

Dependent repos count: 22.2%

Maintainers (2)

jmchilton mvdbeek

Last synced: 6 months ago

pypi.org: galaxy-web-apps

Galaxy web apps

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-web-apps.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 28
Dependent Packages: 2
Dependent Repositories: 1
Downloads: 356 Last month

Rankings

Forks count: 1.3%

Stargazers count: 1.9%

Dependent packages count: 7.4%

Average: 11.1%

Dependent repos count: 22.2%

Downloads: 22.6%

Maintainers (2)

jmchilton mvdbeek

Last synced: 6 months ago

pypi.org: galaxy-test-api

Galaxy API tests

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-test-api.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 31
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 286 Last month

Rankings

Forks count: 1.3%

Stargazers count: 1.9%

Dependent packages count: 7.4%

Average: 11.3%

Dependent repos count: 22.2%

Downloads: 23.7%

Maintainers (2)

jmchilton mvdbeek

Last synced: 6 months ago

pypi.org: galaxy-navigation

Galaxy client DOM navigation framework

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-navigation.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 28
Dependent Packages: 2
Dependent Repositories: 0
Downloads: 559 Last month

Rankings

Forks count: 1.3%

Stargazers count: 1.9%

Dependent packages count: 7.3%

Average: 13.0%

Downloads: 13.1%

Dependent repos count: 41.3%

Maintainers (1)

mvdbeek

Last synced: 6 months ago

pypi.org: galaxy-tours

Galaxy tours backend framework

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-tours.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 28
Dependent Packages: 1
Dependent Repositories: 0
Downloads: 518 Last month

Rankings

Forks count: 1.3%

Stargazers count: 1.9%

Dependent packages count: 7.3%

Average: 13.1%

Downloads: 13.7%

Dependent repos count: 41.3%

Maintainers (1)

mvdbeek

Last synced: 6 months ago

pypi.org: galaxy-test-selenium

Galaxy Selenium Tests

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-test-selenium.readthedocs.io/
License: AFL
Latest release: 22.1.1
published over 3 years ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 29 Last month

Rankings

Forks count: 1.3%

Stargazers count: 1.9%

Dependent packages count: 7.4%

Average: 13.7%

Dependent repos count: 22.2%

Downloads: 35.4%

Maintainers (2)

jmchilton mvdbeek

Last synced: 6 months ago

conda-forge.org: galaxy-util

Homepage: https://galaxyproject.org
License: AFL-3.0
Latest release: 22.1.1
published over 3 years ago

Versions: 2
Dependent Packages: 2
Dependent Repositories: 0

Rankings

Forks count: 4.9%

Stargazers count: 11.2%

Average: 17.4%

Dependent packages count: 19.5%

Dependent repos count: 34.0%

Last synced: 6 months ago

pypi.org: galaxy-authnz

Galaxy AuthNZ

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-authnz.readthedocs.io/
License: AFL
Latest release: 19.9.0.dev0
published over 4 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 24 Last month

Rankings

Forks count: 1.3%

Stargazers count: 1.9%

Dependent packages count: 7.4%

Average: 19.0%

Dependent repos count: 22.2%

Downloads: 62.0%

Maintainers (2)

jmchilton mvdbeek

Last synced: 6 months ago

pypi.org: galaxy-model-tools

Galaxy Model Tools`

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-model-tools.readthedocs.io/
License: AFL
Latest release: 19.9.0.dev2
published over 4 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 15 Last month

Rankings

Forks count: 1.3%

Stargazers count: 1.9%

Dependent packages count: 7.4%

Average: 19.0%

Dependent repos count: 22.2%

Downloads: 62.0%

Maintainers (2)

jmchilton mvdbeek

Last synced: 6 months ago

conda-forge.org: galaxy-containers

Homepage: https://galaxyproject.org
License: AFL-3.0
Latest release: 22.1.1
published over 3 years ago

Versions: 3
Dependent Packages: 1
Dependent Repositories: 0

Rankings

Forks count: 4.9%

Stargazers count: 11.2%

Average: 19.7%

Dependent packages count: 28.8%

Dependent repos count: 34.0%

Last synced: 6 months ago

pypi.org: galaxy-test-tools

Galaxy Test Tools`

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-test-tools.readthedocs.io/
License: AFL
Latest release: 19.9.0.dev2
published over 4 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 20 Last month

Rankings

Forks count: 1.3%

Stargazers count: 1.9%

Dependent packages count: 7.4%

Average: 20.7%

Dependent repos count: 22.2%

Downloads: 70.9%

Maintainers (2)

jmchilton mvdbeek

Last synced: 6 months ago

conda-forge.org: galaxy-tool-util

Homepage: https://galaxyproject.org
License: AFL-3.0
Latest release: 22.1.5
published over 3 years ago

Versions: 6
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Forks count: 4.9%

Stargazers count: 11.2%

Average: 25.3%

Dependent repos count: 34.0%

Dependent packages count: 51.2%

Last synced: 6 months ago

pypi.org: galaxy-tool-shed-schema

Pydantic models for the Galaxy Tool Shed

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-tool-shed-schema.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 322 Last month

Rankings

Dependent packages count: 9.0%

Average: 29.8%

Dependent repos count: 50.6%

Maintainers (1)

mvdbeek

Last synced: 6 months ago

pypi.org: galaxy-tool-util-models

Pydantic models for Galaxy tools

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-tool-util-models.readthedocs.io/
License: MIT
Latest release: 25.0.2
published 6 months ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 18,537 Last month

Rankings

Dependent packages count: 9.0%

Average: 29.8%

Dependent repos count: 50.6%

Maintainers (1)

mvdbeek

Last synced: 6 months ago

pypi.org: galaxy-web-client

Galaxy web client (frontend)

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-web-client.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 171 Last month

Rankings

Dependent packages count: 9.2%

Average: 30.5%

Dependent repos count: 51.7%

Maintainers (1)

natefoo

Last synced: 6 months ago

pypi.org: galaxy-client

Galaxy web client (frontend)

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-client.readthedocs.io/
License: AFL
Latest release: 25.0.dev0
published 10 months ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 15 Last month

Rankings

Dependent packages count: 9.2%

Average: 30.5%

Dependent repos count: 51.8%

Maintainers (1)

natefoo

Last synced: 6 months ago

pypi.org: galaxy-tool-shed

Galaxy Tool Shed

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-tool-shed.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 17
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 171 Last month

Rankings

Dependent packages count: 9.8%

Average: 37.3%

Dependent repos count: 64.8%

Maintainers (1)

jmchilton

Last synced: 6 months ago

pypi.org: galaxy-schema

Pydantic models for Galaxy

Homepage: https://github.com/galaxyproject/galaxy
Documentation: https://galaxy-schema.readthedocs.io/
License: AFL
Latest release: 25.0.2
published 6 months ago

Versions: 17
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 488 Last month

Rankings

Dependent packages count: 9.8%

Average: 37.3%

Dependent repos count: 64.8%

Maintainers (1)

mvdbeek

Last synced: 6 months ago

Dependencies

.github/workflows/deployment.yaml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/setup-python v4 composite
actions/upload-artifact v2 composite
nanasess/setup-chromedriver v1 composite

.github/workflows/publish_artifacts.yaml actions

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

.github/workflows/setup_selenium.yaml actions

nanasess/setup-chromedriver v2 composite

.github/workflows/test_galaxy_packages_for_pulsar.yaml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/setup-python v4 composite
eWaterCycle/setup-apptainer v2 composite

packages/files/test-requirements.txt pypi

fs-gcsfs * test
pytest * test
s3fs >=2023.1.0,<2024 test

packages/selenium/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/selenium/pyproject.toml pypi

packages/selenium/test-requirements.txt pypi

pytest * test

packages/test_api/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/test_api/pyproject.toml pypi

lib/galaxy/web/proxy/js/Dockerfile docker

node 0.11.13 build

test/functional/tools/realtime/simple/Dockerfile docker

python 2.7 build

config/plugins/visualizations/fits_image_viewer/package.json npm

aladin-lite-galaxy ^1.0.0
cpy-cli ^5.0.0
parcel-bundler ^1.4.1

config/plugins/visualizations/h5web/package.json npm

parcel ^2.9.3 development
@h5web/app ^8.0.0
buffer ^6.0.3
normalize.css ^8.0.1
react 18.2.0
react-dom 18.2.0

lib/galaxy/web/proxy/js/package.json npm

commander ~2.20.3
eventemitter3 3.1.2
http-proxy 1.18.1
node-watch 0.7.0
sqlite3 4.2.0

lib/tool_shed/webapp/frontend/package.json npm

@graphql-codegen/cli ^2.16.1 development
@graphql-codegen/client-preset ^1.2.3 development
@quasar/vite-plugin ^1.0.4 development
@types/node ^16.6.1 development
@typescript-eslint/eslint-plugin ^5.47.1 development
@typescript-eslint/parser ^5.47.1 development
@vitejs/plugin-vue ^1.6.0 development
@vue/compiler-sfc ^3.2.6 development
@vue/eslint-config-typescript ^11.0.2 development
concurrently ^7.6.0 development
eslint ^8.30.0 development
eslint-config-prettier ^8.5.0 development
eslint-plugin-prettier ^4.2.1 development
eslint-plugin-vue ^9.8.0 development
eslint-plugin-vuejs-accessibility ^2.0.0 development
prettier ^2.8.1 development
sass ^1.32.0 development
typescript ^4.3.2 development
vite ^4.4.9 development
vue-eslint-parser ^9.1.0 development
vue-tsc ^1.0.16 development
@apollo/client ^3.7.3
@quasar/extras ^1.12.4
@vue/apollo-composable ^4.0.0-beta.1
@vue/apollo-option ^4.0.0-alpha.20
axios ^1.2.1
date-fns ^2.29.3
date-fns-tz ^1.3.7
e ^0.2.2
graphql ^16.6.0
graphql-tag ^2.12.6
openapi-typescript-fetch ^1.1.3
pinia ^2.0.28
quasar ^2.5.0
vue ^3.2.6
vue-router 4

lib/tool_shed/webapp/package.json npm

@galaxyproject/tool-shed-frontend ^0.2.1

package.json npm

@galaxyproject/galaxy-client ^23.1.1
cpy-cli ^5.0.0

lib/galaxy/dependencies/conditional-requirements.txt pypi

azure-storage ==0.32.0
boto3 *
chronos-python ==1.2.1
custos-sdk *
drmaa *
fluent-logger *
fs-basespace *
fs-gcsfs *
fs.anvilfs *
fs.dropboxfs >=1.0
fs.googledrivefs *
fs.onedatarestfs *
fs.sshfs *
fs.webdavfs >=0.4.2
galaxycloudrunner *
google-cloud-storage >=2.8.0
hvac *
influxdb *
kamaki *
ldap3 ==2.9.1
mysqlclient *
pbs_python *
pkce *
psycopg2-binary ==2.9.5
pygithub *
pykube ==0.15.0
python-gitlab >=2.10.0
python-irodsclient ==1.1.3
python-ldap ==3.4.0
python-pam *
sentry-sdk *
statsd *
tensorflow ==2.9.3
total-perspective-vortex >=2.3.2,<3
watchdog *
weasyprint *

lib/galaxy/dependencies/dev-requirements.txt pypi

aiohttp ==3.9.1 development
aiosignal ==1.3.1 development
alabaster ==0.7.13 development
amqp ==5.2.0 development
anyio ==4.1.0 development
ase ==3.22.1 development
async-timeout ==4.0.3 development
attrs ==23.1.0 development
axe-selenium-python ==2.1.6 development
babel ==2.14.0 development
backports-zoneinfo ==0.2.1 development
billiard ==4.2.0 development
black ==23.12.0 development
build ==1.0.3 development
cachecontrol ==0.13.1 development
celery ==5.3.6 development
certifi ==2023.11.17 development
cffi ==1.16.0 development
charset-normalizer ==3.3.2 development
click ==8.1.7 development
click-didyoumean ==0.3.0 development
click-plugins ==1.1.1 development
click-repl ==0.3.0 development
codespell ==2.2.6 development
colorama ==0.4.6 development
contourpy ==1.1.1 development
coverage ==7.3.3 development
cryptography ==41.0.7 development
cwltest ==2.4.20231031143732 development
cycler ==0.12.1 development
darker ==1.7.2 development
defusedxml ==0.7.1 development
deprecated ==1.2.14 development
docutils ==0.18.1 development
exceptiongroup ==1.2.0 development
filelock ==3.13.1 development
fluent-logger ==0.10.0 development
fonttools ==4.46.0 development
frozenlist ==1.4.1 development
galaxy-release-util ==0.1.5 development
greenlet ==3.0.1 development
h11 ==0.14.0 development
httpcore ==1.0.2 development
httpx ==0.25.2 development
idna ==3.6 development
imagesize ==1.4.1 development
importlib-metadata ==7.0.0 development
importlib-resources ==6.1.1 development
iniconfig ==2.0.0 development
isodate ==0.6.1 development
isort ==5.13.2 development
jaraco-classes ==3.3.0 development
jeepney ==0.8.0 development
jinja2 ==3.1.2 development
junit-xml ==1.9 development
keyring ==24.3.0 development
kiwisolver ==1.4.5 development
kombu ==5.3.4 development
lxml ==4.9.3 development
markdown-it-py ==3.0.0 development
markdown-it-reporter ==0.0.2 development
markupsafe ==2.1.3 development
matplotlib ==3.7.4 development
matplotlib ==3.8.2 development
mdit-py-plugins ==0.4.0 development
mdurl ==0.1.2 development
mirakuru ==2.5.2 development
mistune ==2.0.5 development
more-itertools ==10.1.0 development
msgpack ==1.0.7 development
multidict ==6.0.4 development
mypy-extensions ==1.0.0 development
myst-parser ==2.0.0 development
nh3 ==0.2.15 development
numpy ==1.24.4 development
numpy ==1.26.2 development
outcome ==1.3.0.post0 development
packaging ==23.2 development
pathspec ==0.12.1 development
pillow ==10.1.0 development
pkce ==1.0.3 development
pkginfo ==1.9.6 development
platformdirs ==4.1.0 development
playwright ==1.40.0 development
pluggy ==1.3.0 development
port-for ==0.7.2 development
prettytable ==3.9.0 development
prompt-toolkit ==3.0.43 development
psutil ==5.9.6 development
psycopg ==3.1.15 development
pycparser ==2.21 development
pyee ==11.0.1 development
pygithub ==2.1.1 development
pygments ==2.17.2 development
pyjwt ==2.8.0 development
pynacl ==1.5.0 development
pyparsing ==3.1.1 development
pyproject-hooks ==1.0.0 development
pysocks ==1.7.1 development
pytest ==7.4.3 development
pytest-asyncio ==0.23.2 development
pytest-base-url ==2.0.0 development
pytest-celery ==0.0.0 development
pytest-cov ==4.1.0 development
pytest-html ==4.1.1 development
pytest-httpserver ==1.0.8 development
pytest-json-report ==1.5.0 development
pytest-metadata ==3.0.0 development
pytest-mock ==3.12.0 development
pytest-playwright ==0.4.3 development
pytest-postgresql ==5.0.0 development
pytest-shard ==0.1.2 development
python-dateutil ==2.8.2 development
python-irodsclient ==1.1.9 development
python-slugify ==8.0.1 development
pytz ==2023.3.post1 development
pywin32-ctypes ==0.2.2 development
pyyaml ==6.0.1 development
rdflib ==6.3.2 development
readme-renderer ==42.0 development
requests ==2.31.0 development
requests-toolbelt ==1.0.0 development
responses ==0.24.1 development
rfc3986 ==2.0.0 development
rich ==13.7.0 development
ruamel-yaml ==0.18.5 development
ruamel-yaml-clib ==0.2.8 development
schema-salad ==8.5.20231201181309 development
scipy ==1.10.1 development
scipy ==1.11.4 development
secretstorage ==3.3.3 development
selenium ==4.16.0 development
seletools ==1.4.0 development
setuptools ==69.0.2 development
six ==1.16.0 development
sniffio ==1.3.0 development
snowballstemmer ==2.2.0 development
sortedcontainers ==2.4.0 development
sphinx ==7.1.2 development
sphinx-rtd-theme ==1.3.0 development
sphinxcontrib-applehelp ==1.0.4 development
sphinxcontrib-devhelp ==1.0.2 development
sphinxcontrib-htmlhelp ==2.0.1 development
sphinxcontrib-jquery ==4.1 development
sphinxcontrib-jsmath ==1.0.1 development
sphinxcontrib-qthelp ==1.0.3 development
sphinxcontrib-serializinghtml ==1.1.5 development
statsd ==4.0.1 development
testfixtures ==7.2.2 development
text-unidecode ==1.3 development
tinydb ==4.8.0 development
toml ==0.10.2 development
tomli ==2.0.1 development
trio ==0.23.2 development
trio-websocket ==0.11.1 development
tuspy ==1.0.3 development
twill ==3.2.1 development
twine ==4.0.2 development
typing-extensions ==4.9.0 development
tzdata ==2023.3 development
urllib3 ==1.26.18 development
vine ==5.1.0 development
watchdog ==3.0.0 development
wcwidth ==0.2.12 development
werkzeug ==3.0.1 development
wrapt ==1.16.0 development
wsproto ==1.2.0 development
yarl ==1.9.4 development
zipp ==3.17.0 development

lib/galaxy/dependencies/lint-requirements.txt pypi

flake8 *
flake8-bugbear *
ruff *

packages/job_execution/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/job_execution/pyproject.toml pypi

packages/job_execution/test-requirements.txt pypi

pytest * test

packages/job_metrics/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/job_metrics/pyproject.toml pypi

packages/objectstore/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/objectstore/pyproject.toml pypi

packages/objectstore/test-requirements.txt pypi

pytest * test

packages/package-dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/schema/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/schema/pyproject.toml pypi

packages/schema/test-requirements.txt pypi

pytest * test

packages/job_metrics/test-requirements.txt pypi

pytest * test

packages/meta/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/meta/pyproject.toml pypi

packages/meta/test-requirements.txt pypi

pytest * test

packages/navigation/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/navigation/pyproject.toml pypi

packages/navigation/test-requirements.txt pypi

pytest * test

lib/galaxy/dependencies/pinned-lint-requirements.txt pypi

attrs ==23.1.0
flake8 ==6.1.0
flake8-bugbear ==23.12.2
mccabe ==0.7.0
pycodestyle ==2.11.1
pyflakes ==3.1.0
ruff ==0.1.8

lib/galaxy/dependencies/pinned-requirements.txt pypi

a2wsgi ==1.9.0
adal ==1.2.7
aiobotocore ==2.9.0
aiodataloader ==0.4.0
aiofiles ==23.2.1
aiohttp ==3.9.1
aioitertools ==0.11.0
aiosignal ==1.3.1
alembic ==1.13.0
amqp ==5.2.0
aniso8601 ==9.0.1
anyio ==4.1.0
apispec ==6.3.0
appdirs ==1.4.4
arcp ==0.2.1
argcomplete ==3.2.1
async-timeout ==4.0.3
attmap ==0.13.2
attrs ==23.1.0
babel ==2.14.0
backports-zoneinfo ==0.2.1
bagit ==1.8.1
bagit-profile ==1.3.1
bcrypt ==4.1.2
bdbag ==1.7.1
beaker ==1.12.1
billiard ==4.2.0
bioblend ==1.2.0
bleach ==6.1.0
boltons ==23.1.1
boto ==2.49.0
botocore ==1.33.13
bx-python ==0.10.0
cachecontrol ==0.13.1
celery ==5.3.6
certifi ==2023.11.17
cffi ==1.16.0
charset-normalizer ==3.3.2
cheetah3 ==3.2.6.post1
circus ==0.18.0
click ==8.1.7
click-didyoumean ==0.3.0
click-plugins ==1.1.1
click-repl ==0.3.0
cloudauthz ==0.6.0
cloudbridge ==3.2.0
colorama ==0.4.6
coloredlogs ==15.0.1
conda-package-streaming ==0.9.0
cryptography ==41.0.7
cwl-upgrader ==1.2.11
cwl-utils ==0.32
cwltool ==3.1.20231207110929
decorator ==5.1.1
defusedxml ==0.7.1
deprecation ==2.1.0
dictobj ==0.4
dnspython ==2.4.2
docopt ==0.6.2
docutils ==0.18.1
dparse ==0.6.3
ecdsa ==0.18.0
edam-ontology ==1.25.2
email-validator ==2.1.0.post1
exceptiongroup ==1.2.0
fastapi ==0.98.0
fastapi-utils ==0.2.1
filelock ==3.13.1
frozenlist ==1.4.1
fs ==2.4.16
fsspec ==2023.12.2
future ==0.18.3
galaxy-sequence-utils ==1.1.5
galaxy2cwl ==0.1.4
graphene ==3.3
graphene-sqlalchemy ==3.0.0b3
graphql-core ==3.2.3
graphql-relay ==3.2.0
gravity ==1.0.4
greenlet ==3.0.1
gunicorn ==21.2.0
gxformat2 ==0.18.0
h11 ==0.14.0
h5grove ==1.3.0
h5py ==3.10.0
humanfriendly ==10.0
idna ==3.6
importlib-metadata ==7.0.0
importlib-resources ==6.1.1
isa-rwval ==0.10.10
isodate ==0.6.1
jinja2 ==3.1.2
jmespath ==1.0.1
jsonref ==1.1.0
jsonschema ==4.20.0
jsonschema-specifications ==2023.11.2
kombu ==5.3.4
lagom ==2.6.0
lxml ==4.9.3
mako ==1.3.0
markdown ==3.5.1
markdown-it-py ==3.0.0
markupsafe ==2.1.3
mdurl ==0.1.2
mercurial ==6.6.1
mistune ==2.0.5
mrcfile ==1.4.3
msal ==1.26.0
msgpack ==1.0.7
multidict ==6.0.4
mypy-extensions ==1.0.0
networkx ==2.5
nodeenv ==1.8.0
numpy ==1.24.4
numpy ==1.26.2
oauthlib ==3.2.2
orjson ==3.9.10
oyaml ==1.0
packaging ==23.2
paramiko ==3.3.1
parsley ==1.3
paste ==3.7.1
pastedeploy ==3.1.0
pebble ==5.0.5
pkgutil-resolve-name ==1.3.10
promise ==2.3
prompt-toolkit ==3.0.43
prov ==1.5.1
psutil ==5.9.6
pulsar-galaxy-lib ==0.15.5
pyasn1 ==0.5.1
pycparser ==2.21
pycryptodome ==3.19.0
pydantic ==1.10.13
pydantic-tes ==0.1.5
pydot ==1.4.2
pyeventsystem ==0.1.0
pyfaidx ==0.7.2.2
pygments ==2.17.2
pyjwt ==2.8.0
pykwalify ==1.8.0
pylibmagic ==0.5.0
pynacl ==1.5.0
pyparsing ==3.1.1
pyreadline3 ==3.4.1
pysam ==0.22.0
python-dateutil ==2.8.2
python-jose ==3.3.0
python-magic ==0.4.27
python-multipart ==0.0.6
python3-openid ==3.2.0
pytz ==2023.3.post1
pyyaml ==6.0.1
pyzmq ==25.1.2
rdflib ==6.3.2
referencing ==0.32.0
refgenconf ==0.12.2
regex ==2023.10.3
repoze-lru ==0.7
requests ==2.31.0
requests-oauthlib ==1.3.1
requests-toolbelt ==1.0.0
requests-unixsocket ==0.3.0
rich ==13.7.0
rocrate ==0.9.0
routes ==2.5.1
rpds-py ==0.13.2
rsa ==4.9
ruamel-yaml ==0.18.5
ruamel-yaml-clib ==0.2.8
s3fs ==2023.12.2
schema-salad ==8.5.20231201181309
setuptools ==69.0.2
setuptools-scm ==5.0.2
shellescape ==3.8.1
six ==1.16.0
sniffio ==1.3.0
social-auth-core ==4.0.3
sortedcontainers ==2.4.0
spython ==0.3.13
sqlalchemy ==1.4.50
sqlitedict ==2.1.0
sqlparse ==0.4.4
starlette ==0.27.0
starlette-context ==0.3.6
starlette-graphene3 ==0.6.0
supervisor ==4.2.5
svgwrite ==1.4.3
tenacity ==8.2.3
tifffile ==2023.7.10
tinydb ==4.8.0
tomli ==2.0.1
tornado ==6.4
tqdm ==4.66.1
tuspy ==1.0.3
tuswsgi ==0.5.5
typing-extensions ==4.9.0
tzdata ==2023.3
tzlocal ==5.2
ubiquerg ==0.6.3
urllib3 ==1.26.18
uvicorn ==0.24.0.post1
uvloop ==0.19.0
vine ==5.1.0
wcwidth ==0.2.12
webencodings ==0.5.1
webob ==1.8.7
whoosh ==2.7.4
wrapt ==1.16.0
yacman ==0.9.2
yarl ==1.9.4
zipp ==3.17.0
zipstream-new ==1.1.8
zstandard ==0.22.0

lib/galaxy/dependencies/pinned-typecheck-requirements.txt pypi

cffi ==1.16.0
cryptography ==41.0.7
mypy ==1.7.1
mypy-extensions ==1.0.0
pycparser ==2.21
pydantic ==1.10.13
tomli ==2.0.1
types-bleach ==6.1.0.1
types-boto ==2.49.18.9
types-contextvars ==2.4.7.3
types-dataclasses ==0.6.6
types-docutils ==0.20.0.3
types-markdown ==3.5.0.3
types-paramiko ==3.3.0.2
types-pkg-resources ==0.1.3
types-python-dateutil ==2.8.19.14
types-pyyaml ==6.0.12.12
types-requests ==2.31.0.6
types-six ==1.16.21.9
types-urllib3 ==1.26.25.14
typing-extensions ==4.9.0

lib/galaxy/job_execution/setup.py pypi

packages/app/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/app/pyproject.toml pypi

packages/app/test-requirements.txt pypi

mock-ssh-server * test
pkce * test
pykwalify * test
pytest * test
testfixtures * test

packages/auth/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/auth/pyproject.toml pypi

packages/auth/test-requirements.txt pypi

pytest * test

packages/config/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/config/pyproject.toml pypi

packages/config/test-requirements.txt pypi

gravity >=1.0 test
pytest * test

packages/data/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/data/pyproject.toml pypi

packages/data/test-requirements.txt pypi

pytest * test

packages/files/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/files/pyproject.toml pypi

packages/test_api/test-requirements.txt pypi

pytest * test

packages/test_base/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/test_base/pyproject.toml pypi

packages/test_base/test-requirements.txt pypi

pytest * test

packages/test_driver/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/test_driver/pyproject.toml pypi

packages/test_driver/test-requirements.txt pypi

pytest * test

packages/test_selenium/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/test_selenium/pyproject.toml pypi

packages/test_selenium/test-requirements.txt pypi

pytest * test

packages/tool_shed/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/tool_shed/pyproject.toml pypi

packages/tool_shed/test-requirements.txt pypi

pytest * test

packages/tool_util/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/tool_util/pyproject.toml pypi

packages/tool_util/test-requirements.txt pypi

Beaker * test
pytest * test
pytest-mock * test

packages/tours/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/tours/pyproject.toml pypi

packages/tours/test-requirements.txt pypi

pytest * test

packages/util/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/util/pyproject.toml pypi

packages/util/test-requirements.txt pypi

pytest * test
pytest-httpserver * test
responses * test

packages/web_apps/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/web_apps/pyproject.toml pypi

packages/web_apps/test-requirements.txt pypi

httpx * test
pytest * test
pytest-asyncio * test

packages/web_framework/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/web_framework/pyproject.toml pypi

packages/web_framework/test-requirements.txt pypi

pytest * test

packages/web_stack/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/web_stack/pyproject.toml pypi

packages/web_stack/test-requirements.txt pypi

gunicorn * test
pytest * test

pyproject.toml pypi

Babel *
Beaker *
Cheetah3 !=3.2.6.post2
Mako *
Markdown *
MarkupSafe *
Mercurial *
Parsley *
Paste *
PyJWT *
PyYAML *
Routes *
SQLAlchemy >=1.4.25,<2
WebOb *
Whoosh *
a2wsgi *
aiofiles *
alembic *
apispec *
bdbag >=1.6.3
bioblend *
bleach *
boltons *
boto *
bx-python *
celery *
circus *
cloudauthz ==0.6.0
cloudbridge *
conda-package-streaming *
cwltool >=3.1.20230624081518
dictobj *
dnspython *
docutils !=0.17, !=0.17.1
dparse *
edam-ontology *
fastapi >=0.71.0, !=0.89.0, <0.99
fastapi-utils *
fs *
future *
galaxy_sequence_utils *
graphene-sqlalchemy 3.0.0b3
gravity >=1.0.4
gunicorn *
gxformat2 *
h5grove >=1.2.1
h5py *
importlib-resources *
isa-rwval >=0.10.10
kombu >=5.3
lagom *
mrcfile *
msal *
nodeenv *
numpy *
packaging *
paramiko !=2.9.0, !=2.9.1
pebble *
psutil *
pulsar-galaxy-lib >=0.15.0.dev0
pycryptodome *
pydantic <2
pykwalify *
pylibmagic *
pyparsing *
pysam >=0.21
python >=3.8,<3.12
python-dateutil *
python-magic *
python-multipart *
refgenconf >=0.12.0
regex *
requests *
rocrate *
s3fs ^2023.1.0
schema-salad !=8.3.20220721194857
social-auth-core ==4.0.3
sortedcontainers *
sqlitedict *
sqlparse *
starlette *
starlette-context *
starlette-graphene3 *
svgwrite *
tifffile *
tuswsgi *
typing-extensions *
uvicorn *
uvloop *
zipstream-new *

requirements.txt pypi

a2wsgi ==1.9.0
adal ==1.2.7
aiobotocore ==2.9.0
aiodataloader ==0.4.0
aiofiles ==23.2.1
aiohttp ==3.9.1
aioitertools ==0.11.0
aiosignal ==1.3.1
alembic ==1.13.0
amqp ==5.2.0
aniso8601 ==9.0.1
anyio ==4.1.0
apispec ==6.3.0
appdirs ==1.4.4
arcp ==0.2.1
argcomplete ==3.2.1
async-timeout ==4.0.3
attmap ==0.13.2
attrs ==23.1.0
babel ==2.14.0
backports-zoneinfo ==0.2.1
bagit ==1.8.1
bagit-profile ==1.3.1
bcrypt ==4.1.2
bdbag ==1.7.1
beaker ==1.12.1
billiard ==4.2.0
bioblend ==1.2.0
bleach ==6.1.0
boltons ==23.1.1
boto ==2.49.0
botocore ==1.33.13
bx-python ==0.10.0
cachecontrol ==0.13.1
celery ==5.3.6
certifi ==2023.11.17
cffi ==1.16.0
charset-normalizer ==3.3.2
cheetah3 ==3.2.6.post1
circus ==0.18.0
click ==8.1.7
click-didyoumean ==0.3.0
click-plugins ==1.1.1
click-repl ==0.3.0
cloudauthz ==0.6.0
cloudbridge ==3.2.0
colorama ==0.4.6
coloredlogs ==15.0.1
conda-package-streaming ==0.9.0
cryptography ==41.0.7
cwl-upgrader ==1.2.11
cwl-utils ==0.32
cwltool ==3.1.20231207110929
decorator ==5.1.1
defusedxml ==0.7.1
deprecation ==2.1.0
dictobj ==0.4
dnspython ==2.4.2
docopt ==0.6.2
docutils ==0.18.1
dparse ==0.6.3
ecdsa ==0.18.0
edam-ontology ==1.25.2
email-validator ==2.1.0.post1
exceptiongroup ==1.2.0
fastapi ==0.98.0
fastapi-utils ==0.2.1
filelock ==3.13.1
frozenlist ==1.4.1
fs ==2.4.16
fsspec ==2023.12.2
future ==0.18.3
galaxy-sequence-utils ==1.1.5
galaxy2cwl ==0.1.4
graphene ==3.3
graphene-sqlalchemy ==3.0.0b3
graphql-core ==3.2.3
graphql-relay ==3.2.0
gravity ==1.0.4
greenlet ==3.0.1
gunicorn ==21.2.0
gxformat2 ==0.18.0
h11 ==0.14.0
h5grove ==1.3.0
h5py ==3.10.0
humanfriendly ==10.0
idna ==3.6
importlib-metadata ==7.0.0
importlib-resources ==6.1.1
isa-rwval ==0.10.10
isodate ==0.6.1
jinja2 ==3.1.2
jmespath ==1.0.1
jsonref ==1.1.0
jsonschema ==4.20.0
jsonschema-specifications ==2023.11.2
kombu ==5.3.4
lagom ==2.6.0
lxml ==4.9.3
mako ==1.3.0
markdown ==3.5.1
markdown-it-py ==3.0.0
markupsafe ==2.1.3
mdurl ==0.1.2
mercurial ==6.6.1
mistune ==2.0.5
mrcfile ==1.4.3
msal ==1.26.0
msgpack ==1.0.7
multidict ==6.0.4
mypy-extensions ==1.0.0
networkx ==2.5
nodeenv ==1.8.0
numpy ==1.24.4
numpy ==1.26.2
oauthlib ==3.2.2
orjson ==3.9.10
oyaml ==1.0
packaging ==23.2
paramiko ==3.3.1
parsley ==1.3
paste ==3.7.1
pastedeploy ==3.1.0
pebble ==5.0.5
pkgutil-resolve-name ==1.3.10
promise ==2.3
prompt-toolkit ==3.0.43
prov ==1.5.1
psutil ==5.9.6
pulsar-galaxy-lib ==0.15.5
pyasn1 ==0.5.1
pycparser ==2.21
pycryptodome ==3.19.0
pydantic ==1.10.13
pydantic-tes ==0.1.5
pydot ==1.4.2
pyeventsystem ==0.1.0
pyfaidx ==0.7.2.2
pygments ==2.17.2
pyjwt ==2.8.0
pykwalify ==1.8.0
pylibmagic ==0.5.0
pynacl ==1.5.0
pyparsing ==3.1.1
pyreadline3 ==3.4.1
pysam ==0.22.0
python-dateutil ==2.8.2
python-jose ==3.3.0
python-magic ==0.4.27
python-multipart ==0.0.6
python3-openid ==3.2.0
pytz ==2023.3.post1
pyyaml ==6.0.1
pyzmq ==25.1.2
rdflib ==6.3.2
referencing ==0.32.0
refgenconf ==0.12.2
regex ==2023.10.3
repoze-lru ==0.7
requests ==2.31.0
requests-oauthlib ==1.3.1
requests-toolbelt ==1.0.0
requests-unixsocket ==0.3.0
rich ==13.7.0
rocrate ==0.9.0
routes ==2.5.1
rpds-py ==0.13.2
rsa ==4.9
ruamel-yaml ==0.18.5
ruamel-yaml-clib ==0.2.8
s3fs ==2023.12.2
schema-salad ==8.5.20231201181309
setuptools ==69.0.2
setuptools-scm ==5.0.2
shellescape ==3.8.1
six ==1.16.0
sniffio ==1.3.0
social-auth-core ==4.0.3
sortedcontainers ==2.4.0
spython ==0.3.13
sqlalchemy ==1.4.50
sqlitedict ==2.1.0
sqlparse ==0.4.4
starlette ==0.27.0
starlette-context ==0.3.6
starlette-graphene3 ==0.6.0
supervisor ==4.2.5
svgwrite ==1.4.3
tenacity ==8.2.3
tifffile ==2023.7.10
tinydb ==4.8.0
tomli ==2.0.1
tornado ==6.4
tqdm ==4.66.1
tuspy ==1.0.3
tuswsgi ==0.5.5
typing-extensions ==4.9.0
tzdata ==2023.3
tzlocal ==5.2
ubiquerg ==0.6.3
urllib3 ==1.26.18
uvicorn ==0.24.0.post1
uvloop ==0.19.0
vine ==5.1.0
wcwidth ==0.2.12
webencodings ==0.5.1
webob ==1.8.7
whoosh ==2.7.4
wrapt ==1.16.0
yacman ==0.9.2
yarl ==1.9.4
zipp ==3.17.0
zipstream-new ==1.1.8
zstandard ==0.22.0

.github/workflows/api.yaml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/setup-python v4 composite
actions/upload-artifact v3 composite
codecov/codecov-action v3 composite
postgres 13 docker

.github/workflows/build_container_image.yaml actions

actions-hub/docker master composite
actions-hub/docker/login master composite
actions/checkout v3 composite

.github/workflows/check_test_class_names.yaml actions

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

.github/workflows/codeql-analysis.yml actions

actions/checkout v3 composite
github/codeql-action/analyze v2 composite
github/codeql-action/autobuild v2 composite
github/codeql-action/init v2 composite

.github/workflows/converter_tests.yaml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/setup-python v4 composite
actions/upload-artifact v3 composite

.github/workflows/cwl_conformance.yaml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/setup-python v4 composite
actions/upload-artifact v3 composite
codecov/codecov-action v3 composite
postgres 13 docker

.github/workflows/db_indexes.yaml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/setup-python v4 composite
postgres ${{ matrix.postgresql-version }} docker

.github/workflows/dependencies.yaml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/setup-python v4 composite
peter-evans/create-pull-request v4 composite

.github/workflows/docs.yaml actions

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