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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
author goeckslab
date Sat, 21 Jun 2025 15:06:22 +0000
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650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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1 # Galaxy-Ludwig
650639a4a75f 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.
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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3
650639a4a75f 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.
650639a4a75f 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.
650639a4a75f 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).
650639a4a75f 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:
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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9 ```
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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10 <section id="ludwig" name="Ludwig Applications">
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11 <tool file="ludwig/ludwig_evaluate.xml" />
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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12 <tool file="ludwig/ludwig_experiment.xml" />
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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13 <tool file="ludwig/ludwig_hyperopt.xml" />
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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14 <tool file="ludwig/ludwig_predict.xml" />
650639a4a75f 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" />
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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16 <tool file="ludwig/ludwig_train.xml" />
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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17 <tool file="ludwig/ludwig_visualize.xml" />
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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18 </section>
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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19 ```
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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650639a4a75f 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:
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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24 ```
650639a4a75f 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
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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28 workers: 4
650639a4a75f 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:
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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32 local:
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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33 runner: local
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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34 docker_enabled: true
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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35 ```
650639a4a75f 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.
650639a4a75f 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.
650639a4a75f 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.
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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40 # Get Galaxy-Ludwig docker image
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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42 This step is optional.
650639a4a75f 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:
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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44 ```
650639a4a75f 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
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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46 ```
650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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650639a4a75f planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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48 * Should be good to go.