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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
author goeckslab
date Sat, 21 Jun 2025 15:04:30 +0000
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e3c63770083d planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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1 # Galaxy-Ludwig
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2 A library of Galaxy deep learning tools based on Ludwig.
e3c63770083d planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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3
e3c63770083d 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.
e3c63770083d 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.
e3c63770083d 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).
e3c63770083d 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:
e3c63770083d planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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9 ```
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10 <section id="ludwig" name="Ludwig Applications">
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11 <tool file="ludwig/ludwig_evaluate.xml" />
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12 <tool file="ludwig/ludwig_experiment.xml" />
e3c63770083d planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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13 <tool file="ludwig/ludwig_hyperopt.xml" />
e3c63770083d planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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14 <tool file="ludwig/ludwig_predict.xml" />
e3c63770083d 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" />
e3c63770083d planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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16 <tool file="ludwig/ludwig_train.xml" />
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17 <tool file="ludwig/ludwig_visualize.xml" />
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18 </section>
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19 ```
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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:
e3c63770083d planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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24 ```
e3c63770083d 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
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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:
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33 runner: local
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34 docker_enabled: true
e3c63770083d planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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35 ```
e3c63770083d 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.
e3c63770083d 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.
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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.
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40 # Get Galaxy-Ludwig docker image
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e3c63770083d planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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42 This step is optional.
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43 If you want to speed up your runs, execute the following command:
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44 ```
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45 docker pull quay.io/goeckslab/galaxy-ludwig-gpu:0.10.1
e3c63770083d planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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46 ```
e3c63770083d planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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e3c63770083d planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
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48 * Should be good to go.