Personal tools

Galaxy File Uploads

From UABgrid Documentation

Revision as of 20:23, 29 July 2012 by (Talk | contribs)

Jump to: navigation, search

UAB Galaxy supports data import in three ways:

  1. Direct file uploads to using a web browser
  2. Fetching data from external URLs
  3. Importing existing files on Cheaha file system

Web browser based file upload is convenient approach, but not recommended for files larger than 1 GB in size because of browser limitations. Also, web browser based upload in Galaxy doesn't provide any feedback on upload progress and can be an unreliable operation. You can fetch data from external URL locations, but that's not an efficient operation. Hence, it's recommended to use last option where files can be imported from Cheaha file system. You can transfer files to Cheaha using tools like SCP and later import these files in Galaxy application. You will need an account on Cheaha cluster to transfer files to it. Please refer to Cheaha_GettingStarted#Access page for getting an account on it. Following sections provides an overview of methods to import existing Cheaha files into Galaxy.

Galaxy provides two options to import data on the filesystem:

  1. FTP or file drop-off mode: Galaxy provides FTP upload option in the UI to import files from a user's FTP directory. Although Galaxy call this FTP upload method, it doesn't really require any FTP setup to upload files. The 'FTP upload' option should be considered as 'FTP or file drop-off' type mode, where files dropped in a directory can be 'moved' into Galaxy application. When Galaxy imports files from 'FTP or drop-off' directory, the original file in is deleted. On UAB Galaxy platform we have configured this directory as '/lustre/importfs/galaxy/$USER' and you can get your files in this directory using scp, wget or any other transfer mechanisms. See Galaxy_FTP_Upload page for more details on this data import method.
  2. Data Library: Galaxy has a concept of 'Data Libraries' which provide a data container to organize your data in a hierarchical manner, similar to directories on a desktop. Data libraries provide other features for data organization and sharing as well. Data libraries support direct files uploads from a web browser, data fetch from external URLs and also file system imports. The file system import options is similar to FTP option described above, however, it doesn't delete original file on the file system after it has been imported in Galaxy. On UAB Galaxy platform we have configured Galaxy to import files in '/lustre/scratch/$USER' directory if the user configures appropriate permissions for Galaxy application. You can get your files in '/lustre/scratch/$USER' directory using scp, wget or any other transfer mechanisms. See Galaxy_Data_Library_Import page for more details on this data import method.