Galaxy File Uploads

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Attention: Research Computing Documentation has Moved

Please use the new documentation url for all Research Computing documentation needs.

As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.

Thank you,

The Research Computing Team

UAB Galaxy supports data import in three ways:

Method Limitation
Direct file uploads to using a web browser only files < 2G
Fetching data from external URLs through Galaxy (ftp/http) can't access some password protected sites, such as the HudsonAlpha GSL
Importing files via the Cheaha file system requires an account on cheaha, but command-line can be avoided


Do not store sensitive information on this filesystem. It is not encrypted. Note that your data will be stored on the cluster filesystem, and while not accessible to ordinary users, it could be accessible to the cluster administrator(s).

Direct file uploads to using a web browser

Web browser based file upload is a convenient approach, but not recommended for files larger than 2 GB in size because of browser limitations. Also, web browser based upload in Galaxy doesn't provide any feedback on upload progress and it can be an unreliable operation. Hence, it's recommended to stage data on Galaxy accessible file-system and then import it in Galaxy.

Importing files via the Cheaha file system

UAB Galaxy instance is configured to look for files in '/scratch/importfs/galaxy/$USER' and '/scratch/user/$USER' directories on Cheaha. Data files can be copied to Cheaha using scp or they can be downloaded using tools like wget, curl or ftp. A nice windows-friendly drag-and-drop tool is WinSCP. Please refer to Cheaha_GettingStarted#Access page for getting access to Cheaha.

Following sections provide an overview of UAB Galaxy import methods.

  1. importfs or file drop-off mode: UAB Galaxy platform is configured to import files in $GALAXY_IMPORTFS directory on Cheaha (/scratch/importfs/galaxy/$USER). Galaxy application 'moves' files from imports directory to it's internal datasets directory. See Galaxy_Importfs page for more details on this upload method.
  2. Data Library: Galaxy has a concept of 'Data Libraries' which is a data container to organize files in an hierarchical manner, similar to directories on a desktop. Data libraries provide other features for data organization and sharing as well. Data libraries support files uploads using a web browser, fetching from external URLs and also by copying existing directories in a file-system. The file-system copy is similar to importfs option described above, however, it copies file to internal datasets directory rather than moving it. UAB Galaxy platform is configured to copy files in $USER_SCRATCH (/scratch/user/$USER) directory. See Galaxy_Data_Libraries page for more details on data libraries.