News Brief

24/10/2012 - Wolfpack Cluster's launched! Check out the User Guide now!

Garvan Galaxy User Guide

DEPRECATED PLEASE VISIT

DEPRECATED PLEASE VISIT

IMPORTANT: Backup your data first

  1. For data residing in the Galaxy FTP (such as from Ramaciotti or uploaded yourself)
    • Download your data by connecting to the Galaxy FTP (instructions below).
  2. For data, imported or otherwise, in a Galaxy history (ie a Dataset)
    • Use the “Download” button (floppy disk icon) for the Dataset.

NOTE that once data is imported into a Galaxy history (via “Get Data → Upload File”) it will be moved from the FTP server and into Galaxy as a Dataset.

Upload and Download Data via FTP

Galaxy allows users to upload big data (2GB+) into their histories via FTP. To connect to the FTP server, a FTP client is needed. We currently support WinSCP on Windows, Cyberduck on Apple Mac and generic Linux ftp command.

URL Port Mode Credential
ftp.pwbc.garvan.unsw.edu.au 10022 Passive Galaxy Account

:!: Please make sure the size of the data you are going to FTP is not exceeding your Galaxy quota (300GB).

:!: Make sure the username you use for the ftp is exactly the same case as your Galaxy login.

Windows


The WinSCP should work out of the box. If not, please check that it is able to connect via passive mode:

Apple Mac

Linux Command Line

Downloading multiple files using WGET

:!: Replace items in <..>

# Download everything 
wget -r -nH ftp://ftp.pwbc.garvan.unsw.edu.au:10022/  --user <galaxy email> --ask-password
# Download everything in the remote folder ''mysamples/one''. Local folder structure would be ''./mysamples/one/''
wget -r -nH ftp://ftp.pwbc.garvan.unsw.edu.au:10022/mysamples/one/  --user <galaxy email> --ask-password
# Download everything in the folder ''mysamples/one''.  Local folder structure would be ''./one/''
wget -r -nH --cut-dirs=1 ftp://ftp.pwbc.garvan.unsw.edu.au:10022/mysamples/one/  --user <galaxy email> --ask-password

Uploading multiple files via command line LFTP

# Mirror a local directory to the remote ftp folder
cd <directory with files>
lftp -e "mirror -v -R ./ <dest_dir>; exit" ftp.pwbc.garvan.unsw.edu.au -p 10022 -u <galaxy email>

# More advanced options
lftp -e "mirror -v -R -P <parallel number> -i <inc. files with regex> <source_dir> <dest_dir>; exit" ftp.pwbc.garvan.unsw.edu.au -p 10022 -u <galaxy email>

Uploading and downloading multiple files via command line FTP

ftp -p ftp.pwbc.garvan.unsw.edu.au 10022

Toggle off interactive mode

prompt

Use mput or mget to move files using a pattern match.

Eg. To download a file FROM ftp

mget files_* 

Eg. To put a file from local dir INTO ftp

mput files_* 

Import FTP data into a History

Once the data are uploaded to the FTP server, it's ready for importing to the Galaxy history via Get Data → Upload File:

Deleting data

Datasets which have not been permanently deleted will count towards your quota. Permanently delete them to free up space.

Ways of showing deleted (but not permanently deleted) data

  • [From the History side panel] “Options (cog wheel) → Show Deleted Datasets”
  • [From the Saved History page] “Advanced Search” → “status: all”