Galaxy File Uploads
https://docs.rc.uab.edu/
Please use the new documentation url https://docs.rc.uab.edu/ 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 |
| Importing existing files on Cheaha file system | requires an account on cheaha |
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.
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 [wikipedia:Secure_copy scp] or they can be downloaded using tools like wget, curl or ftp. Please refer to Cheaha_GettingStarted#Access page for getting access to Cheaha.
Following sections provide an overview of UAB Galaxy import methods.
- 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.
- 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.