Galaxy File Uploads

From UABgrid Documentation
(Difference between revisions)
Jump to: navigation, search
m
(updated ftp related to sections with importfs and revised other sections aswell)
Line 4: Line 4:
 
# Importing existing files on Cheaha file system
 
# Importing existing files on Cheaha file system
  
Web browser based file upload is a 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 it can be an unreliable operation. You can fetch data from external URL locations through Galaxy, but that's not an efficient operation. Hence, it's recommended to use the last option where files can be imported from [[Cheaha]] file system. You can transfer files to Cheaha using  tools like [http://en.wikipedia.org/wiki/Secure_copy 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
+
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. You can fetch data from external URL locations through Galaxy, but that's not an efficient operation. Hence, it's recommended to stage data on Galaxy accessible file-system and then import it in Galaxy.
[[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:
+
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.
# 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.  
+
 
# 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.
+
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 '/scratch/importfs/galaxy/$USER' directory. Galaxy application 'moves' files from imports directory to it's internal datasets directory. See [[Galaxy_Data_Import]] page for more details on the importfs method.
 +
# Data Library: Galaxy has a concept of 'Data Libraries' which is a data container to organize files in an hierarchical manner, similar to directories on a desktop. Data libraries provide other features for data organization and sharing as well. Data libraries support direct files uploads from a web browser, data fetch from external URLs and also file system imports. The file system import options is similar to FTP option described above, however, it doesn't delete original file on the file system after it has been imported in Galaxy. UAB Galaxy platform is configured to import files in '/scratch/user/$USER' directory. See [[Galaxy_Data_Library_Import]] page for more details on this data import method.

Revision as of 20:15, 7 March 2013

UAB Galaxy supports data import in three ways:

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

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. You can fetch data from external URL locations through Galaxy, but that's not an efficient 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.

  1. importfs or file drop-off mode: UAB Galaxy platform is configured to import files in '/scratch/importfs/galaxy/$USER' directory. Galaxy application 'moves' files from imports directory to it's internal datasets directory. See Galaxy_Data_Import page for more details on the importfs method.
  2. Data Library: Galaxy has a concept of 'Data Libraries' which is a data container to organize files in an hierarchical manner, similar to directories on a desktop. Data libraries provide other features for data organization and sharing as well. Data libraries support direct files uploads from a web browser, data fetch from external URLs and also file system imports. The file system import options is similar to FTP option described above, however, it doesn't delete original file on the file system after it has been imported in Galaxy. UAB Galaxy platform is configured to import files in '/scratch/user/$USER' directory. See Galaxy_Data_Library_Import page for more details on this data import method.
Personal tools
Namespaces

Variants
Actions
Navigation
Toolbox