Sitting in the NeLS workshop at CBU right now:

• NeLS starting page (NeLS = Norwegian e-Infrastructure for LifeScience research)
• NeLS is funded by Elixir.no
• You can log in with your FEIDE (University account)
• NeLS storage is NeLS's cloud storage solution

There are 5 different instances of Galaxy (Bergen, Tromsø, Trondheim, Oslo and Aas) in NeLS, which we all can use but they don't share the history between them.

• There is also long-term storage called StoreBioInfo
• TSD is for sensitive data
• Check the Help button to contact support.
• First task: upload a file from your local hard drive:
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• We can also share data using NeLS
• support <at> bioinfo <dot> no can add users to projects.
• Shared data is found under My Projects:

• Now we can start doing serious analyses
• Copying data from shared directory to my own, by copy-paste
• Go to available pipelines
• Click Available Pipelines and choose RNA-seq pipeline in Trondheim
• Now we are going to Galaxy
• 

• Now we can select data to import using Get Data -> Get files

• Then data appears in history.
• You better don't use Internet Exploder

• There's a lot of tools in Galaxy.... in the left menu
• lick: NGS: QC and manipulation

  Choose FastQC FastQC:Read QC reports using FastQC

  

   

• Create two datase-collections:

• 

• Running TopHat2
• We need to annotate the DataType first from fastq to fastqsanger
• 
• Galaxy is a bit picky about file types
• "Why did I have to do that???"
• Now the Tool can be run....
• 
• Jobs are NOT running but queued ....
• 
• Pipelines run several tools in a row automatically
• Workflows can be imported from "Shared Data" Menu (not from Workflow menu!)
• 
• Hit Run from the little wheel
• Set parameters.... running
• 
• Get some coffeee.... while waiting
• You may now log out
• When you come back, you can load your history from History options -> saved histories
• David shared the result with me in NeLS storage -> My projects -> final_results
• 
• There are 5 instances of Galaxy in NeLS with different specialties. Galaxy Instances don't share histories.
• There are different levels of storage in NeLS as well, you are responsible for moving your data.

• David demonstrates how to use ssh and scp to log in and transfer files. You most likely need a Mac or Linux.
• Windows users need to use sftp clients, any ftp client should do. Putty might also work, ro FileZilla.