pulsar-app

Distributed job execution application built for Galaxy

https://github.com/galaxyproject/pulsar

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
○
DOI references
○
Academic publication links
✓
Committers with academic emails
4 of 27 committers (14.8%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (17.0%) to scientific vocabulary

Keywords from Contributors

cloudman usegalaxy

Last synced: 6 months ago · JSON representation ·

Repository

Distributed job execution application built for Galaxy

Basic Info

Host: GitHub
Owner: galaxyproject
License: apache-2.0
Language: Python
Default Branch: master
Homepage: https://pulsar.readthedocs.io
Size: 2.8 MB

Statistics

Stars: 39
Watchers: 24
Forks: 54
Open Issues: 89
Releases: 10

Created over 11 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation

README.rst

.. figure:: https://galaxyproject.org/images/galaxy-logos/pulsar_transparent.png
   :alt: Pulsar Logo

.. image:: https://readthedocs.org/projects/pulsar/badge/?version=latest
   :target: http://pulsar.readthedocs.io/en/latest/?badge=latest
   :alt: Documentation Status
.. image:: https://badge.fury.io/py/pulsar-app.svg
   :target: https://pypi.python.org/pypi/pulsar-app/
   :alt: Pulsar on the Python Package Index (PyPI)
.. image:: https://travis-ci.org/galaxyproject/pulsar.png?branch=master
   :target: https://travis-ci.org/galaxyproject/pulsar
   :alt: Build Status
.. image:: https://coveralls.io/repos/galaxyproject/pulsar/badge.png?branch=master
   :target: https://coveralls.io/r/galaxyproject/pulsar?branch=master
   :alt: Test Coverage

This project is a Python server application that allows a `Galaxy
`_ server to run jobs on remote systems (including
Windows) without requiring a shared mounted file systems. Unlike traditional
Galaxy job runners - input files, scripts, and config files may be transferred
to the remote system, the job is executed, and the results are transferred back
to the Galaxy server - eliminating the need for a shared file system.

Full documentation for the project can be found on `Read The Docs
`_.

------------------
Configuring Galaxy
------------------

Galaxy job runners are configured in Galaxy's ``job_conf.xml`` file. Some small
examples of how to configure this can be found `here
`__, but be sure
to check out ``job_conf.xml.sample_advanced`` in your Galaxy code base or on
`Github
`_
for complete information.

------------------
Quickstart
------------------

Full details on different ways to install Pulsar can be found in the `install
section `__ of the
documentaiton, but if your machine has the proper Python dependencies
available it can be quickly download and a test job run with::

    $ mkdir pulsar
    $ cd pulsar
    $ python3 -m venv venv
    $ . venv/bin/activate    # venv\Scripts\activate.bat on Windows
    $ pip install 'pulsar-app[web]'
    $ pulsar-config
    $ pulsar --daemon        # just `pulsar` on Windows
    $ pulsar-check           # runs a test job

Please note that as of the 0.14.0 release, Pulsar no longer supports any version
of Python 2. The minimum supported Python version is 3.5.

The `configuration documentation
`__
has many details on securing your Pulsar server and enabling advanced features
such as cluster integration and message queue communication.

-----------------------
Development and Testing
-----------------------

The recommended approach to setting up a development environment for Pulsar on
Linux or macOS is rougly as follows::

    $ git clone https://github.com/galaxyproject/pulsar
    $ cd pulsar
    $ python3 -m venv .venv
    $ . .venv/bin/activate    # .venv\Scripts\activate on Windows
    $ pip install -e '.[web]'
    $ pip install -r dev-requirements.txt

The ``-e`` flag to ``pip`` installs Pulsar in "editable" mode, meaning that
changes you make to the source code will be reflected when running the pulsar
commands installed in the virtual environment.

This project is distributed with unit and integration tests (many of which will
not run under Windows), the following command will install the needed python
components to run these tests. The following command will then run these tests::

    $ make tests

The following command will then produce a coverage report corresponding to this
test and place it in the ``coverage_html_report`` subdirectory of this
project.::

    $ coverage html

Check out the `Contributing
`_ documentation
for many more details on developing and contributing to Pulsar.

Please note that this project is released with a `Contributor Code of Conduct 
`__. By participating
in this project you agree to abide by its terms.

-----------------------
Support
-----------------------

This documentation is an incomplete work in progress. There are more ways to
configure and use Pulsar than are documented, and a growing number of Pulsar
experts who would be more than happy to answer your questions and help with any
problems you may run in to while setting up a Pulsar deployment. Please do not
hesitate to reach out on the `Galaxy Admins Gitter Channel`_

.. _Galaxy Admins Gitter Channel: https://gitter.im/galaxyproject/admins

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)

To cite the Pulsar in publications, please use:

...wait the Pulsar is unpublished. I guess just use the source code URL for
now.

I do hope to work on an Pulsar publication in the next couple months
however, though I am completely clueless about how to approach
this. If you have any advice on this please help me out.

Should I do a application focused methods paper on some Galaxy-P tools
that would not otherwise be usable in Galaxy without the Pulsar geared at
proteomics researchers, should I do a short application note about the
technical aspects of the Pulsar? Both? Combine concepts into one paper
with two audiences?  What journal(s) should I target? Thanks!

GitHub Events

Total

Create event: 6
Release event: 2
Issues event: 14
Watch event: 1
Delete event: 2
Issue comment event: 41
Push event: 35
Pull request review comment event: 12
Pull request review event: 21
Pull request event: 31
Fork event: 3

Last Year

Create event: 6
Release event: 2
Issues event: 14
Watch event: 1
Delete event: 2
Issue comment event: 41
Push event: 35
Pull request review comment event: 12
Pull request review event: 21
Pull request event: 31
Fork event: 3

Committers

Last synced: 10 months ago

All Time

Total Commits: 1,398
Total Committers: 27
Avg Commits per committer: 51.778
Development Distribution Score (DDS): 0.245

Past Year

Commits: 45
Committers: 4
Avg Commits per committer: 11.25
Development Distribution Score (DDS): 0.378

Top Committers

Name	Email	Commits
John Chilton	j**n@g**m	1,055
Nate Coraor	n**e@b**u	112
mvdbeek	m**k@g**m	102
Björn Grüning	b**n@g**u	24
nuwang	2****g	20
Eric Rasche	r**c@y**u	18
Nicola Soranzo	n**o@e**k	18
Enis Afgan	a**e@g**m	11
Gianmauro Cuccuru	g**o@g**m	7
Yakubov, Sergey	y**s@o**v	4
Dannon	d**r@g**m	4
Rémi Marenco	r**o@g**m	3
Helena Rasche	h**r@h**g	3
Martin Cech	c**n@g**m	2
Daniel Blankenberg	d**g@g**m	2
Manuel Pasieka	m**a@v**t	2
Adrià Cereto Massagué	s**m@g**m	1
Alex Muller	a**x@m**t	1
Andreas Skorczyk	me@a****e	1
Cameron Hyde	c**e@n**m	1
Karthikeyan Singaravelan	t**i@g**m	1
Kyle Ellrott	k**t@g**m	1
Pedro Martinez	p****t	1
Trevor Wennblom	t****r	1
Vahid	V****i	1
Inge Alexander Raknes	i**s@u**o	1
cat-bro	c**b@g**m	1

Committer Domains (Top 20 + Academic)

uit.no: 1 neoformit.com: 1 andreas-sk.de: 1 mullr.net: 1 vbcf.ac.at: 1 hx42.org: 1 ornl.gov: 1 earlham.ac.uk: 1 yandex.ru: 1 gruenings.eu: 1 bx.psu.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 76
Total pull requests: 118
Average time to close issues: over 2 years
Average time to close pull requests: about 2 months
Total issue authors: 24
Total pull request authors: 13
Average comments per issue: 2.37
Average comments per pull request: 0.92
Merged pull requests: 82
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 14
Pull requests: 31
Average time to close issues: N/A
Average time to close pull requests: 29 days
Issue authors: 7
Pull request authors: 8
Average comments per issue: 0.0
Average comments per pull request: 0.61
Merged pull requests: 18
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

natefoo (28)
jmchilton (12)
hexylena (7)
bgruening (3)
peterg1t (3)
cat-bro (3)
gmauro (2)
mvdbeek (2)
neoformit (1)
peterjc (1)
zsalvet (1)
AliNemat (1)
martindemko (1)
simonbray (1)
potant (1)

Pull Request Authors

mvdbeek (36)
jmchilton (35)
natefoo (17)
nuwang (10)
nsoranzo (5)
kysrpex (4)
martenson (3)
BorisYourich (2)
neoformit (2)
cat-bro (1)
gecage952 (1)
gregvonkuster (1)
peterg1t (1)

Top Labels

Issue Labels

enhancement (5) confirmed bug (4) documentation missing (2) test missing (1) help wanted (1) usegalaxy.org (1)

Pull Request Labels

confirmed bug (8) enhancement (5) test missing (1) possible bug (1)

Packages

Total packages: 3
Total downloads:
- pypi 11,646 last-month
Total docker downloads: 3,926

Total dependent packages: 2
(may contain duplicates)
Total dependent repositories: 54
(may contain duplicates)
Total versions: 128
Total maintainers: 4

pypi.org: pulsar-galaxy-lib

Distributed job execution application built for Galaxy (http://galaxyproject.org/).

Homepage: https://github.com/galaxyproject/pulsar
Documentation: https://pulsar-galaxy-lib.readthedocs.io/
License: Apache License 2.0
Latest release: 0.15.9
published 8 months ago

Versions: 61
Dependent Packages: 2
Dependent Repositories: 50
Downloads: 11,409 Last month
Docker Downloads: 3,926

Rankings

Docker downloads count: 1.6%

Downloads: 1.9%

Dependent repos count: 2.1%

Dependent packages count: 3.2%

Average: 4.2%

Forks count: 5.9%

Stargazers count: 10.6%

Maintainers (3)

jmchilton mvdbeek nsoranzo

Last synced: 6 months ago

pypi.org: pulsar-app

Distributed job execution application built for Galaxy (http://galaxyproject.org/).

Homepage: https://github.com/galaxyproject/pulsar
Documentation: https://pulsar-app.readthedocs.io/
License: Apache License 2.0
Latest release: 0.15.9
published 8 months ago

Versions: 66
Dependent Packages: 0
Dependent Repositories: 4
Downloads: 237 Last month

Rankings

Forks count: 5.9%

Dependent repos count: 7.5%

Dependent packages count: 10.0%

Average: 10.1%

Stargazers count: 10.5%

Downloads: 16.4%

Maintainers (3)

jmchilton mvdbeek nsoranzo

Last synced: 6 months ago

spack.io: py-pulsar-galaxy-lib

Distributed job execution application built for Galaxy (http://galaxyproject.org/).

Homepage: https://github.com/galaxyproject/pulsar
License: []
Latest release: 0.14.16
published about 3 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent repos count: 0.0%

Forks count: 16.2%

Stargazers count: 23.2%

Average: 24.2%

Dependent packages count: 57.3%

Maintainers (1)

adamjstewart

Last synced: 6 months ago

Dependencies

dev-requirements.txt pypi

coverage *
flake8 *
kombu *
mypy *
pycurl *
pyflakes *
pykube *
pytest *
sphinx ==1.2
stopit *
twine *
types-PyYAML *
types-paramiko *
types-pkg-resources *
types-psutil *
types-pycurl *
types-requests *
webtest *
wheel *

requirements.txt pypi

PasteDeploy *
galaxy-job-metrics >=19.9.0.dev1
galaxy-objectstore >=19.9.0.dev1
galaxy-tool-util >=19.9.0.dev3
galaxy-util >=19.9.0.dev1
paramiko *
psutil *
pyyaml *
webob *

.github/workflows/galaxy_framework.yaml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/setup-python v2 composite
actions/upload-artifact v2 composite
postgres 13 docker

.github/workflows/pulsar.yaml actions

actions/checkout v2 composite
actions/setup-python v3 composite

docker/coexecutor/Dockerfile docker

conda/miniconda3 latest build

docker/cvmfs/Dockerfile docker

conda/miniconda2 latest build

docker/testing/Dockerfile docker

ubuntu 14.04 build

docs/requirements.txt pypi

sphinx >=2
sphinx-rtd-theme >=0.5.2

setup.py pypi