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)
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.
In the top menu click the username @traineeXX (on the right)
Click Dashboard
LabID Dashboard
Reach the User Dashboard from the top menu
On the User Dashboard, click the Configure galaxy... button. This will open the Galaxy API key setup pop-up.
I do not see the button.
If the Configure galaxy... is not shown, you may have already set up the Galaxy API key. You should then see a green checkmark with the URL to the configured Galaxy instance. You may reconfigure using the button. This may be needed if your API key changed.
Galaxy API key configuration is done
In the pop-up
Galaxy API key setup pop-up
- Paste your API key
- Click the Save button
Galaxy API key configuration is done
Your API key is now configured. LabID knows how to communicate with Galaxy.
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
Add data using the dropbox: select a single bam file and your personal Study
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
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.
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
Synced data in the Galaxy library
This data can be imported to a history by selecting the file(s) and clicking **Export to History->as Datasets"
Galaxy history
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.
Tags
Each Galaxy dataset has multiple tags starting with LabID:. These tags, show the LabID ID of a Dataset and the DatafileCopy. As these tags are inheritable, they are set on every newly derived dataset in Galaxy. This allows us to always find back the original dataset underlying the final derived dataset.
