Distributed job execution application built for Galaxy (http://galaxyproject.org/).
.. 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 <http://galaxyproject.org>_ 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 <https://pulsar.readthedocs.io/>_.
Galaxy job runners are configured in Galaxy's job_conf.xml file. Some small
examples of how to configure this can be found here <https://pulsar.readthedocs.org/en/latest/galaxy_conf.html>__, but be sure
to check out job_conf.xml.sample_advanced in your Galaxy code base or on
Github <https://github.com/galaxyproject/galaxy/blob/master/config/job_conf.xml.sample_advanced>_
for complete information.
Full details on different ways to install Pulsar can be found in the install section <https://pulsar.readthedocs.org/en/latest/install.html>__ 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 <https://pulsar.readthedocs.org/en/latest/configure.html>__
has many details on securing your Pulsar server and enabling advanced features
such as cluster integration and message queue communication.
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 <https://pulsar.readthedocs.org/en/latest/contributing.html>_ documentation
for many more details on developing and contributing to Pulsar.
Please note that this project is released with a Contributor Code of Conduct <https://pulsar.readthedocs.org/en/latest/conduct.html>__. By participating
in this project you agree to abide by its terms.
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
.. to_doc
Pull Request 351_@mvdbeek).
Pull Request 338@natefoo). Pull Request 332@mvdbeek). Pull Request 337@cat-bro). Pull Request 334ConnectionResetError. Pull Request 331_@SergeyYakubov). Pull Request 321Pull Request 324_Pull Request 325_Pull Request 306_Pull Request 302_Pull Request 302_amqp_key_prefix to direct task queue naming while retaining simple
default manager names and such in container scheduling deployments. Pull Request 315_Pull Request 312, Pull Request 319Pull Request 318_Pull Request 318_Pull Request 297_Pull Request 322_Pull Request 303_@natefoo). Pull Request 301@mvdbeek). Pull Request 299@natefoo). Pull Request 287Manager (thanks
to @nsoranzo).
Pull Request 295metadata_strategy: extended (thanks to @mvdbeek).
Pull Request 294Pull Request 274_Pull Request 271_Pull Request 270_galaxy.json files. Pull Request 269_Pull Request 266_@mvdbeek). Pull Request 264Pull Request 262_@mvdbeek). Pull Request 259Pull Request 261_@natefoo).
Pull Request 257@natefoo). Pull Request 256Pull Request 246_Pull Request 242_@gmauro). Pull Request 232Pull Request 230_@gmauro).
Pull Request 229Pull Request 228_Issue 227_
Pull Request 231_Pull Request 231_@bgruening). Pull Request 226@tirkarthi). Issue 224 Pull Request 225_Pull Request 223_Pull Request 221_Pull Request 228_@bgruening). Pull Request 226@gmauro). Pull Request 213@mvdbeek). Pull Request 216@tirkarthi). Pull Request 225Pull Request 217_Pull Request 218, Pull Request 219Pull Request 202_Pull Request 203_Pull Request 201_Pull Request 187_Dockerfile for Pulsar with CVMFS (thanks to @nuwang_ and @afgane).
Pull Request 166_Pull Request 190_Pull Request 186_@bgruening).
Pull Request 189@dannon).
Pull Request 185@AndreasSko).
Pull Request 184@VJalili).
Pull Request 181Pull Request 180_Pull Request 176, Pull Request 178Pull Request 175_assertEquals() (thanks to @nsoranzo). Pull Request 173_Pull Request 174_Pull Request 177_Pull Request 157_Pull Request 159_Pull Request 160_Pull Request 164_Pull Request 165_Pull Request 170_@mvdbeek). Pull Request 172Pull Request 156_Pull Request 145_Pull Request 146, Pull Request 153Pull Request 148_Pull Request 149_$GALAXY_VIRTUAL_ENV and $PRESERVE_GALAXY_ENVIRONMENT. Fix remote
metadata in cases where the tool environment changes the python on
$PATH. Pull Request 137_Pull Request 141_jobs_directory destination param Pull Request 136_Pull Request 130_conda_auto_* option resolution and include a sample
dependency_resolvers_conf.xml (thanks to @mapa17). Pull Request 132_Pull Request 138, Pull Request 139,
Pull Request 140_Pull Request 143_Pull Request 124, Issue 123Makefile command for setup.py develop. fd82d00_galaxy-lib Python package instead of
manually synchronizing Python files across Pulsar and Galaxy.Pull Request 82_ 431088c_Pull Request 78, Pull Request 80Pull Request 84_Pull Request 73_Issue 72_Pull Request 62_pulsar-main and pulsar-config commands as scripts. 9d43ae0_pulsar-run script for issues commands against a Pulsar server (experimental). 3cc7f74_Pull Request <https://github.com/galaxyproject/pulsar/pull/34>__pip/setup.py-style
installs.BitBucket <https://bitbucket.org/jmchilton/lwr>__.announcement <http://dev.list.galaxyproject.org/New-Remote-Job-Runner-td4138951.html>__
and initial commit <https://github.com/galaxyproject/pulsar/commit/163ed48d5a1902ceb84c38f10db8cbe5a0c1039d>__... github_links
.. _Pull Request 351: https://github.com/galaxyproject/pulsar/pull/351 .. _Pull Request 338: https://github.com/galaxyproject/pulsar/pull/338 .. _Pull Request 332: https://github.com/galaxyproject/pulsar/pull/332 .. _Pull Request 337: https://github.com/galaxyproject/pulsar/pull/337 .. _Pull Request 334: https://github.com/galaxyproject/pulsar/pull/334 .. _Pull Request 331: https://github.com/galaxyproject/pulsar/pull/331 .. _Pull Request 321: https://github.com/galaxyproject/pulsar/pull/321 .. _Pull Request 325: https://github.com/galaxyproject/pulsar/pull/325 .. _Pull Request 324: https://github.com/galaxyproject/pulsar/pull/324 .. _Pull Request 322: https://github.com/galaxyproject/pulsar/pull/322 .. _Pull Request 318: https://github.com/galaxyproject/pulsar/pull/318 .. _Pull Request 319: https://github.com/galaxyproject/pulsar/pull/319 .. _Pull Request 312: https://github.com/galaxyproject/pulsar/pull/312 .. _Pull Request 315: https://github.com/galaxyproject/pulsar/pull/315 .. _Pull Request 306: https://github.com/galaxyproject/pulsar/pull/306 .. _Pull Request 297: https://github.com/galaxyproject/pulsar/pull/297 .. _Pull Request 302: https://github.com/galaxyproject/pulsar/pull/302 .. _Pull Request 303: https://github.com/galaxyproject/pulsar/pull/303 .. _Pull Request 301: https://github.com/galaxyproject/pulsar/pull/301 .. _Pull Request 299: https://github.com/galaxyproject/pulsar/pull/299 .. _Pull Request 295: https://github.com/galaxyproject/pulsar/pull/295 .. _Pull Request 294: https://github.com/galaxyproject/pulsar/pull/294 .. _Pull Request 287: https://github.com/galaxyproject/pulsar/pull/287 .. _Pull Request 271: https://github.com/galaxyproject/pulsar/pull/271 .. _Pull Request 274: https://github.com/galaxyproject/pulsar/pull/274 .. _Pull Request 270: https://github.com/galaxyproject/pulsar/pull/270 .. _Pull Request 269: https://github.com/galaxyproject/pulsar/pull/269 .. _Pull Request 266: https://github.com/galaxyproject/pulsar/pull/266 .. _Pull Request 264: https://github.com/galaxyproject/pulsar/pull/264 .. _Pull Request 262: https://github.com/galaxyproject/pulsar/pull/262 .. _Pull Request 259: https://github.com/galaxyproject/pulsar/pull/259 .. _Pull Request 261: https://github.com/galaxyproject/pulsar/pull/261 .. _Pull Request 257: https://github.com/galaxyproject/pulsar/pull/257 .. _Pull Request 256: https://github.com/galaxyproject/pulsar/pull/256 .. _Pull Request 246: https://github.com/galaxyproject/pulsar/pull/246 .. _Pull Request 242: https://github.com/galaxyproject/pulsar/pull/242 .. _Pull Request 232: https://github.com/galaxyproject/pulsar/pull/232 .. _Pull Request 230: https://github.com/galaxyproject/pulsar/pull/230 .. _Pull Request 229: https://github.com/galaxyproject/pulsar/pull/229 .. _Pull Request 228: https://github.com/galaxyproject/pulsar/pull/228 .. _Pull Request 231: https://github.com/galaxyproject/pulsar/pull/231 .. _Issue 227: https://github.com/galaxyproject/pulsar/issues/227 .. _Pull Request 226: https://github.com/galaxyproject/pulsar/pull/226 .. _Pull Request 225: https://github.com/galaxyproject/pulsar/pull/225 .. _Issue 224: https://github.com/galaxyproject/pulsar/issues/224 .. _Pull Request 228: https://github.com/galaxyproject/pulsar/pull/228 .. _Pull Request 226: https://github.com/galaxyproject/pulsar/pull/226 .. _Pull Request 213: https://github.com/galaxyproject/pulsar/pull/213 .. _Pull Request 216: https://github.com/galaxyproject/pulsar/pull/216 .. _Pull Request 225: https://github.com/galaxyproject/pulsar/pull/225 .. _Pull Request 223: https://github.com/galaxyproject/pulsar/pull/223 .. _Pull Request 217: https://github.com/galaxyproject/pulsar/pull/217 .. _Pull Request 218: https://github.com/galaxyproject/pulsar/pull/218 .. _Pull Request 219: https://github.com/galaxyproject/pulsar/pull/219 .. _Pull Request 221: https://github.com/galaxyproject/pulsar/pull/221 .. _Pull Request 202: https://github.com/galaxyproject/pulsar/pull/202 .. _Pull Request 203: https://github.com/galaxyproject/pulsar/pull/203 .. _Pull Request 201: https://github.com/galaxyproject/pulsar/pull/201 .. _Pull Request 190: https://github.com/galaxyproject/pulsar/pull/190 .. _Pull Request 166: https://github.com/galaxyproject/pulsar/pull/166 .. _Pull Request 186: https://github.com/galaxyproject/pulsar/pull/186 .. _Pull Request 187: https://github.com/galaxyproject/pulsar/pull/187 .. _Pull Request 189: https://github.com/galaxyproject/pulsar/pull/189 .. _Pull Request 185: https://github.com/galaxyproject/pulsar/pull/185 .. _Pull Request 184: https://github.com/galaxyproject/pulsar/pull/184 .. _Pull Request 181: https://github.com/galaxyproject/pulsar/pull/181 .. _Pull Request 180: https://github.com/galaxyproject/pulsar/pull/180 .. _da086c9: https://github.com/galaxyproject/pulsar/commit/da086c9 .. _8bd5511: https://github.com/galaxyproject/pulsar/commit/8bd5511 .. _b6278b4: https://github.com/galaxyproject/pulsar/commit/b6278b4 .. _39de377: https://github.com/galaxyproject/pulsar/commit/39de377 .. _f477bc4: https://github.com/galaxyproject/pulsar/commit/f477bc4 .. _Pull Request 178: https://github.com/galaxyproject/pulsar/pull/178 .. _Pull Request 176: https://github.com/galaxyproject/pulsar/pull/176 .. _Pull Request 173: https://github.com/galaxyproject/pulsar/pull/173 .. _Pull Request 174: https://github.com/galaxyproject/pulsar/pull/174 .. _Pull Request 175: https://github.com/galaxyproject/pulsar/pull/175 .. _Pull Request 177: https://github.com/galaxyproject/pulsar/pull/177 .. _Pull Request 172: https://github.com/galaxyproject/pulsar/pull/172 .. _Pull Request 170: https://github.com/galaxyproject/pulsar/pull/170 .. _Pull Request 165: https://github.com/galaxyproject/pulsar/pull/165 .. _Pull Request 164: https://github.com/galaxyproject/pulsar/pull/164 .. _Pull Request 160: https://github.com/galaxyproject/pulsar/pull/160 .. _Pull Request 159: https://github.com/galaxyproject/pulsar/pull/159 .. _Pull Request 157: https://github.com/galaxyproject/pulsar/pull/157 .. _Pull Request 156: https://github.com/galaxyproject/pulsar/pull/156 .. _Pull Request 145: https://github.com/galaxyproject/pulsar/pull/145 .. _Pull Request 146: https://github.com/galaxyproject/pulsar/pull/146 .. _Pull Request 148: https://github.com/galaxyproject/pulsar/pull/148 .. _Pull Request 149: https://github.com/galaxyproject/pulsar/pull/149 .. _Pull Request 153: https://github.com/galaxyproject/pulsar/pull/153 .. _Pull Request 143: https://github.com/galaxyproject/pulsar/pull/143 .. _Pull Request 141: https://github.com/galaxyproject/pulsar/pull/141 .. _Pull Request 136: https://github.com/galaxyproject/pulsar/pull/136 .. _Pull Request 137: https://github.com/galaxyproject/pulsar/pull/137 .. _Pull Request 140: https://github.com/galaxyproject/pulsar/pull/140 .. _Pull Request 139: https://github.com/galaxyproject/pulsar/pull/139 .. _Pull Request 138: https://github.com/galaxyproject/pulsar/pull/138 .. _Pull Request 132: https://github.com/galaxyproject/pulsar/pull/132 .. _Pull Request 130: https://github.com/galaxyproject/pulsar/pull/130 .. _11ce744: https://github.com/galaxyproject/pulsar/commit/11ce744 .. _3573341: https://github.com/galaxyproject/pulsar/commit/3573341 .. _93ab8a1: https://github.com/galaxyproject/pulsar/commit/93ab8a1 .. _929bffa: https://github.com/galaxyproject/pulsar/commit/929bffa .. _629fdea: https://github.com/galaxyproject/pulsar/commit/629fdea .. _Pull Request 124: https://github.com/galaxyproject/pulsar/pull/124 .. _Issue 123: https://github.com/galaxyproject/pulsar/issues/123 .. _ad33cb9: https://github.com/galaxyproject/pulsar/commit/ad33cb9 .. _d7c524e: https://github.com/galaxyproject/pulsar/commit/d7c524e .. _fd82d00: https://github.com/galaxyproject/pulsar/commit/fd82d00 .. _a985107: https://github.com/galaxyproject/pulsar/commit/a985107 .. _38953f3: https://github.com/galaxyproject/pulsar/commit/38953f3 .. _6f4328e: https://github.com/galaxyproject/pulsar/commit/6f4328e .. _8f7c04a: https://github.com/galaxyproject/pulsar/commit/8f7c04a .. _cadfc5a: https://github.com/galaxyproject/pulsar/commit/cadfc5a .. _d262323: https://github.com/galaxyproject/pulsar/commit/d262323 .. _ce0636a: https://github.com/galaxyproject/pulsar/commit/ce0636a .. _ce9d4f9: https://github.com/galaxyproject/pulsar/commit/ce9d4f9 .. _dc47140: https://github.com/galaxyproject/pulsar/commit/dc47140 .. _7e23d43: https://github.com/galaxyproject/pulsar/commit/7e23d43 .. _60bf962: https://github.com/galaxyproject/pulsar/commit/60bf962 .. _Pull Request 73: https://github.com/galaxyproject/pulsar/pull/73 .. _1017bc5: https://github.com/galaxyproject/pulsar/commit/1017bc5 .. _Pull Request 84: https://github.com/galaxyproject/pulsar/pull/84 .. _140a069: https://github.com/galaxyproject/pulsar/commit/140a069 .. _Pull Request 78: https://github.com/galaxyproject/pulsar/pull/78 .. _Pull Request 80: https://github.com/galaxyproject/pulsar/pull/80 .. _Pull Request 82: https://github.com/galaxyproject/pulsar/pull/82 .. _abbba40: https://github.com/galaxyproject/pulsar/commit/abbba40 .. _00197f2: https://github.com/galaxyproject/pulsar/commit/00197f2 .. _431088c: https://github.com/galaxyproject/pulsar/commit/431088c .. _e8814ae: https://github.com/galaxyproject/pulsar/commit/e8814ae .. _fe3e919: https://github.com/galaxyproject/pulsar/commit/fe3e919 .. _2b3942d: https://github.com/galaxyproject/pulsar/commit/2b3942d .. _fa2b6dc: https://github.com/galaxyproject/pulsar/commit/fa2b6dc .. _0c61bd9: https://github.com/galaxyproject/pulsar/commit/0c61bd9 .. _86f95ce: https://github.com/galaxyproject/pulsar/commit/86f95ce .. _Issue 72: https://github.com/galaxyproject/pulsar/issues/72 .. _3cc7f74: https://github.com/galaxyproject/pulsar/commit/3cc7f74 .. _9d43ae0: https://github.com/galaxyproject/pulsar/commit/9d43ae0 .. _Pull Request 62: https://github.com/galaxyproject/pulsar/pull/62 .. _@dannon: https://github.com/dannon .. _@AndreasSko: https://github.com/AndreasSko .. _@VJalili: https://github.com/VJalili .. _@nuwang: https://github.com/nuwang .. _@afgane: https://github.com/afgane .. _@bgruening: https://github.com/bgruening .. _@gmauro: https://github.com/gmauro .. _@mvdbeek: https://github.com/mvdbeek .. _@tirkarthi: https://github.com/tirkarthi .. _@natefoo: https://github.com/natefoo .. _@nsoranzo: https://github.com/nsoranzo .. _@SergeyYakubov: https://github.com/SergeyYakubov .. _@cat-bro: https://github.com/cat-bro
FAQs
Distributed job execution application built for Galaxy (http://galaxyproject.org/).
We found that pulsar-galaxy-lib demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 4 open source maintainers collaborating on the project.
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