Blog post showcasing Galaxy integration with eLabFTW

content/news/2025-06-30-elabftw-integration/index.md

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+---
+title: "eLabFTW integration"
+date: "2025-06-30"
+tease: "Bring data straight from your lab"
+hide_tease: false
+authors: José Manuel Domínguez
+authors_structured:
+- github: kysrpex
+subsites: [global, all]
+tags: []
+---
+
+[eLabFTW](https://www.elabftw.net/) is a free and open source electronic lab notebook from
+[Deltablot](https://www.deltablot.com/about/). It can keep track of experiments, equipment and materials from a research
+lab. Each lab can either [host their own installation](https://doc.elabftw.net/#introduction) or go for Deltablot's
+[hosted solution](https://www.deltablot.com/elabftw/). A live demo showcasing its features is available [here](https://demo.elabftw.net/).
+
+And from now on, it is integrated with Galaxy! Release 25.0 brings eLabFTW onboard as a file source. This means that
+files attached to eLabFTW [experiments](https://doc.elabftw.net/user-guide.html#experiments) and 
+[resources](https://doc.elabftw.net/user-guide.html#resources) can be imported to
+[histories](https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/history/tutorial.html)
+with just a few clicks. After the analysis is complete, datasets and histories can be exported back as attachments to an
+experiment or resource. 
+
+## Getting started
+
+Before it can be used, the feature _must be enabled by a Galaxy administrator_. Once enabled, navigate to the _Settings_
+page on your eLabFTW server and go to the _API Keys_ tab.   
+
+![eLabFTW API Keys tab on settings page](./elabftw_api_keys.png)
+
+Generate a new API key and copy it. Choose "Read/Write" permissions to enable both importing and exporting data. "Read
+Only" API keys still work for importing data to Galaxy, but they will cause Galaxy to error out when exporting data to
+eLabFTW.    
+
+![Creating a new API key](./elabftw_api_keys_generate.png)
+
+On Galaxy, open the eLabFTW integration settings under user preferences _Manage Information_ > 
+_Your eLabFTW Integration Settings_. Enter the API key you just generated and the URL of your eLabFTW instance and click
+_Save_.
+
+![eLabFTW integration settings on Galaxy](./elabftw_integration_settings.png)
+
+## Importing files to a Galaxy history
+
+To import files from eLabFTW to a Galaxy history, click _Upload_ on the sidebar and then _Choose remote files_. 
+
+![Galay upload tool](upload_tool.png)
+
+![Remote file sources](file_sources.png)
+
+After selecting _eLabFTW_, Galaxy shows two folders, one that contains all experiments and another that contains all
+resources.
+
+![eLabFTW experiments and resources listed by Galaxy](elabftw_experiments_and_resources.png)
+
+Inside each, all experiments or resources are listed as folders. Attached files are located within each of the folders.
+
+![Experiments listed by Galaxy](elabftw_experiments.png)
+
+![Files attached to the microscopy experiment](elabftw_experiment_microscopy.png)
+
+## Exporting histories to eLabFTW
+
+Clicking _Export History to File_ under _History options_ opens the history export screen. There, select _to remote 
+file_, choose a name, and finally use the box _Click to select directory_ to open the remote file source browser. The
+same screen displayed when importing files will be shown, from where you can select a target experiment or resource.
+
+![History export screen](history_export.png)
+
+Keep in mind that you have to create the experiments and resources themselves on eLabFTW beforehand.
+
+## Exporting datasets to eLabFTW
+
+Individual datasets may also be exported with the help of the
+[dataset export](https://usegalaxy.eu/?tool_id=export_remote&version=latest) tool. First, choose the datasets to export
+under the _What would you like to export?_ section. Then click _Select_ under _Directory URI_ to open the remote file
+source browser, which allows to select the target experiment or resource.
+
+![Dataset export tool](dataset_export.png)