eLabFTW integration
Bring data to Galaxy straight from the lab.
eLabFTW is a free and open source electronic lab notebook from Deltablot. It can keep track of experiments, equipment and materials from a research lab. Each lab can either host their own installation or go for Deltablot's hosted solution. A live demo showcasing its features is available here.
And from now on, it is integrated with Galaxy! eLabFTW support has been deployed to usegalaxy.eu, and the file source will be brought onboard to upstream Galaxy in release 25.0. This means that files attached to eLabFTW experiments and resources can be imported to histories 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.
Generate a new API key and copy it. Choose "Read/Write" permissions to enable both importing and exporting data. "Read Only" API keys work for importing data to Galaxy, but not for exporting data to eLabFTW.
On Galaxy, configure a new eLabFTW file source under user preferences Manage Your Repositories > Create > eLabFTW.
Assign a name to your eLabFTW file source, enter the URL to your eLabFTW instance, and enter the API key you just generated. If you are using a "Read Only" API key, disable the toggle "Allow Galaxy to export data to eLabFTW?". Click Create.
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.
After selecting eLabFTW, Galaxy shows two folders, one that contains all experiments and another that contains all resources.
Inside each, all experiments or resources are listed as folders. Attached files are located within each of the folders.
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.
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 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.
