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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
author goeckslab
date Sat, 21 Jun 2025 15:06:00 +0000
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ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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1 # Galaxy-Ludwig
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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2 A library of Galaxy deep learning tools based on Ludwig.
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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3
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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4 # Install Galaxy-Ludwig into Galaxy
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5 We assume that you have Galaxy running and docker installed in your server/laptop.
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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6 * Create a new folder named ludwig(or whatever) under Galaxy’s tools folder.
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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7 * Select and download the branch you want to install and use. Copy all XML, py files under the tools folder in this repo to the ludwig folder(the folder you created in the last step).
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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8 * Update `tool_conf.xml` to include Galaxy-Ludwig. See [documentation](https://docs.galaxyproject.org/en/master/admin/tool_panel.html) for more details. This is an example:
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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9 ```
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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10 <section id="ludwig" name="Ludwig Applications">
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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11 <tool file="ludwig/ludwig_evaluate.xml" />
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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12 <tool file="ludwig/ludwig_experiment.xml" />
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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13 <tool file="ludwig/ludwig_hyperopt.xml" />
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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14 <tool file="ludwig/ludwig_predict.xml" />
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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15 <tool file="ludwig/ludwig_render_config.xml" />
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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16 <tool file="ludwig/ludwig_train.xml" />
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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17 <tool file="ludwig/ludwig_visualize.xml" />
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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18 </section>
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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19 ```
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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22 * This is an example of a `job_conf.yml` file that you can create to enable Docker for a local Galaxy instance where you want Ludwig-related jobs to run:
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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24 ```
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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25 runners:
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26 local:
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27 load: galaxy.jobs.runners.local:LocalJobRunner
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28 workers: 4
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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29 execution:
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30 default: local
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31 environments:
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32 local:
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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33 runner: local
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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34 docker_enabled: true
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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35 ```
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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36 If you are using an older version of Galaxy, then `job_conf.xml` would be something you want to configure instead of `job_conf.yml`. Then you would want to configure destination instead of execution and environment.
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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37 See [documentation](https://docs.galaxyproject.org/en/master/admin/jobs.html#running-jobs-in-containers) for job_conf configuration.
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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38 * If you haven’t set `sanitize_all_html: false` in `galaxy.yml`, please set it to False to enable our HTML report functionality.
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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40 # Get Galaxy-Ludwig docker image
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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42 This step is optional.
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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43 If you want to speed up your runs, execute the following command:
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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44 ```
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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45 docker pull quay.io/goeckslab/galaxy-ludwig-gpu:0.10.1
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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46 ```
ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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ef7124ab6b02 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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48 * Should be good to go.