Galaxy account setup and data-sync¶

20 min
Medium

Overview

It is possible for LabID to communicate with a Galaxy instance. Doing so allows for sending data from LabID to Galaxy and later retrieve (and register) data that has been processed on Galaxy. This walkthrough helps you to

Connect LabID and Galaxy accounts (with an API key)
Send LabID data to Galaxy
Retrieve the analysed data from Galaxy

Step 1 - Galaxy API key¶

Step 1.1 - Obtain your Galaxy API key¶

Go to the User Dashboard
- In the top menu click the username @traineeXX (on the right)
- Then click Dashboard
- Select the tab Galaxy Configuration

LabID Dashboard

Reach the User Dashboard from the top menu

LabID Configure Galaxy

Click on Configure new instance
In the dropdown for URL, select the galaxy instance for which you want to configure the authentication
Then, below the API key field, click Get your API key from Galaxy.... This will take you to the Galaxy instance
After login into the Galaxy instance, navigate to User Preference (Top Menu)
Navigate to Manage API Key

Galaxy training instance at the EMBL

If you are following a training at the EMBL with a Galaxy training instance, login in the Galaxy training instance with your trainee credentials, i.e. same username, password 123456.

Galaxy User Preferences

Galaxy API key panel — Galaxy User Preferences

Click the Create a new key button

Your API key appears in the Current API key panel
Copy this API key

About API Keys

The API key from Galaxy grants anyone or any application access to your Galaxy account. Hence, when we store this key in LabID, LabID can act on your behalf to send and retrieve data from Galaxy. Keep this API key safe, do not share it, unless you trust the application that requires it. You can always generate a new key in Galaxy to protect your account, you will then have to update the key in LabID as well.

Step 1.2 - Store the Galaxy API key in LabID¶

Return to the LabID User Dashboard
Paste your API key
Click the Save button

Your API key is now configured. LabID knows how to communicate with Galaxy.

Step 2 - (Optional) Add some data to LabID¶

For this hands-on we need to add some data to LabID first, if you already followed Register Raw Datasets 102 you can use the data from Study Paired-end WGS Darjeeling Tea genotypes for traineeXX or Paired-end WGS Coffee arabica genotypes for traineeXX

Using the dropbox add the GSM461178_untreat_paired_chr4.bam* file.
Upon the Verify page select a personal study

Add data using the dropbox

Step 3 - Sync data to Galaxy¶

Data of entire assays or studies can be synced to Galaxy. In this hands-on, we want to sync a whole study.

At EMBL

At EMBL, we host a Galaxy instance at https://galaxy.embl.de and you can setup your account similarly as we did in this tutorial. With your own data, you would typically sync your LabID data to a Galaxy library named after your group.

Navigate to the Study Detail page of the Study used in the previous Step. Click the Sync with Galaxy

Study is named Paired-end WGS Darjeeling Tea genotypes for traineeXX or Paired-end WGS Coffee arabica genotypes for traineeXX

Study Detail page - Sync with Galaxy button

Sync with Galaxy button on the Study detail page

On the "Sync with Galaxy" popup, a few options are presented
- The Libray where the data should be transferred. Here we pick GTN - Material
- A folder within this library, either existing ( ), or create a new one with a given name ( ). Give a new name like TraineeXX
- A naming stratagy. Files created within Galaxy will follow the given naming strategy. Here we pick Filename, this will keep the current filename as it was originally named on disk.

Sync with Galaxy pop-up

Naming strategy

Depending on your data, you can choose a different naming strategy. When syncing fastq files, it makes sense to include the readtype in the name, if it is not already in the Dataset name. The <library_name> refers to the linked SequencingLibrary you may have linked to the raw fastq dataset. If on the other hand, you loaded data with already sensible filenames, you can plainly select "Filename" to sync the file as is.

When ready click Sync

This triggers a syncing task. You can view the status of the syncing task on the Task List page.

Task list with successful syncing task

Step 4 - Find and use the data in Galaxy¶

In Galaxy the data becomes available in the library and folder it was synced to. In our case, it can be found in Library / GTN - Material / TraineeXX.

Galaxy Data library

This data can be imported to a history by selecting the file(s) and clicking **Export to History->as Datasets"

Galaxy history

Once your data is in your history, you can start analysing your data. If you are unfamiliar with Galaxy, we suggest you have a look at the great Galaxy training material available online.