Dataset

Import a Galaxy history

Copy this link:

https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/Microbial_tutorials/Galaxy_history_input_files.tar.gz

  • Go to your Galaxy instance. Make sure you are registered and logged in. Refresh the page.
  • Click on the History cog cog icon
  • Select Import from File

history options

  • In the box called Archived History URL, paste in the link address to the Galaxy history (that you copied above).
  • Click Submit
  • Wait a few seconds.
  • Click on the view all histories button histories icon
  • See if the Galaxy history has been imported: it will be called imported from archive: Data
  • Above that pane, click on the Switch to button.
  • Then click Done (in the top left corner).
  • You should now have a list of five files in your current history. We will use these for the Genomics Workshop; or see below for additional files.

files in galaxy history

Additional Galaxy histories

If you are using only part of the Genomics Workshop, you can upload any required histories listed here. Follow the instructions above.

Galaxy history: FastQC

https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/Microbial_tutorials/FastQChistory.tar.gz

Galaxy history: Spades

https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/Microbial_tutorials/Spadeshistory.tar.gz

Galaxy history: Prokka

https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/Microbial_tutorials/Prokkahistory.tar.gz

Galaxy history: Snippy

https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/Microbial_tutorials/Snippyhistory.tar.gz

Galaxy history: Workflows

https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/Microbial_tutorials/Galaxy-History-Workflows-history.tar.gz

Additional files

If you need individual files, you can upload any of the files listed here. The instructions are listed below.

Wildtype reference

  • wildtype.fna

https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/Microbial_tutorials/wildtype.fna

  • wildtype.gbk

https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/Microbial_tutorials/wildtype.gbk

  • wildtype.gff

https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/Microbial_tutorials/wildtype.gff

Mutant Illumina sequence

  • mutant_R1.fastq.gz

https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/Microbial_tutorials/mutant_R1.fastq.gz

  • mutant_R2.fastq.gz

https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/Microbial_tutorials/mutant_R2.fastq.gz

Assembled contigs

  • SPAdes_contigs.fasta

https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/Microbial_tutorials/SPAdes_contigs.fasta

Upload to Galaxy

There are two ways to upload these files to Galaxy. You can either download to your local computer and upload to Galaxy, or you can tell Galaxy to directly upload the file from an external source.

Download and upload:

  • Download required file(s) to your computer.
  • From the Galaxy tool panel, click on Get Data → Upload File
  • Click the Choose local file button
  • Find and select the file you downloaded and click Open
  • Set the Type correctly.
  • Click the Start button.
  • Once the progress bar reaches 100%, click the Close button
  • The file will now upload to your current history.

Or, tell Galaxy to find the file from an external source:

  • From the Galaxy tool panel, click on Get Data → Upload File
  • Click the Paste/Fetch data button
  • Paste the URL into the box.
  • Click the Start button.
  • Once the progress bar reaches 100%, click the Close button
  • The file will now upload to your current history.