iRODS User Guide

Downloading Illumina HiSeq 2500 data with iRODS

*Update-September 2015- We now offer more simple data retrieval using Cyberduck. Visit our Cyberduck download page for instructions. 

Click here to download and start using the java-based iDrop browser (beta version).

After installing iDrop, start the program.  It will prompt you to enter a pass phrase for accessing grid information.  An iDrop grid is a collection of settings including iRODs server, Port, Zone, Username, and Password.

  1. Set up a pass phrase for your iDrop grid information.  This pass phrase will allow you to access any Grids you create.

  2. Click the OK button.

  3. Add a Grid by clicking the “Add Grid” button and entering the following case sensitive information:

  • Host name (DNS) of the server to connect to:  mozart.arl.arizona.edu

  • Port:  1247

  • iRODS zone:  BCFZone

  • iRODS user:  <your iRODS login name from UAGC/BCF>

  • iRODS password:  <your iRODS password from UAGC/BCF>

Click the Save button.

 

You are now ready to begin transferring data.

  1. Select your mozart.arl.arizona.edu grid and click the Login button

  2. You should see a list of Local Directories on the left and iRODs data directories (folders) on the right.

  3. Choose Local Directory C:

  4. Drag a folder from the right side onto the / folder shown under the Local Directory frame.

  5. Make sure that you have write access to the folder you choose to drag data into.

  6. File Transfer progress is shown at the bottom of the window.

 

The icommands package (see below) offers command-line tools for Windows, Mac and Linux users.

Installing icommands

For UA HPC users, run the "module load irods" command to get access to iRODs icommands.

 

To use icommands from ICE, add /genome/ICEbin to your path, or call the commands in the examples below using the full path, for example, /genome/ICEbin/iinit instead of just iinit.

 
1.  Get the icommands package for your platform:
Linux (64 bit) (32 bit)
 
If you have trouble using any of these files, you can follow these Instructions to download and build icommands directly from iRODS.
 
2.  For Windows, follow the instructions on the download page. For Mac and Linux, continue using the instructions here. All platforms will use this configuration information:
 
Enter the host name (DNS) of the server to connect to:  mozart.arl.arizona.edu
Enter the port number:  1247
Enter your irods user name:  <your login name from UAGC/BCF>
Enter your irods zone:  BCFZone
Enter your current iRODS password:  <your password from UAGC/BCF>
 
a.  Unzip (untar) the packages. Place the contents in an appropriate location; for example, a directory in  your $PATH, such as /usr/local/bin .
 
b.  Using the command line interface, browse to the installation directory and run iinit. Answer the prompts for configuration information, using the answers shown above.
 
You only need to perform the installation once. After you are successfully connected you do not need to re-enter your password to use the BCF iRODS data store from that computer unless you logout.
 
icommands Quick Start Examples
 
These sample commands are entered from the command line once icommands have been installed. Read the official iRODS icommand documentation
https://www.irods.org/index.php/icommands for a full description ofthese and other commands.
 
Initiate connection to iRODS
 
Use iinit to initialize icommands and your data store connection. Answer the prompts. This is a one-time step, to initiate an BCF iRODS data store connection. It only needs to be used again if you change configuration details.
 
[laureljo@tikal ~/data]$ iinit
One or more fields in your iRODS environment file (.irodsEnv) are
missing; please enter them.
Enter the host name (DNS) of the server to connect to:mozart.arl.arizona.edu
Enter the port number:1247
Enter your irods user name:laureljo
Enter your irods zone:BCFZone
Those values will be added to your environment file (for use by
other i-commands) if the login succeeds.
 
Enter your current iRODS password:
 
It is important to logout of the iRODS system if you are using a shared computer. To logout, use the iexit command. To login again on the same device, use iinit.
 
List directory contents
Use ils to list the contents of your current working directory.
 
[laureljo@tikal ~/data]$ ils
/BCFZone/home/laureljo:
C- /BCFZone/home/laureljo/110714_L007
C- /BCFZone/home/laureljo/110714_L008
Change to a new directory
 
[laureljo@tikal ~/data]$ icd 110714_L007
[laureljo@tikal ~/data]$ ils
/BCFZone/home/laureljo/110714_L007:
lane7_NoIndex_L007_R1_001.fastq
lane7_NoIndex_L007_R1_002.fastq
lane7_NoIndex_L007_R1_003.fastq
lane7_NoIndex_L007_R1_004.fastq
lane7_NoIndex_L007_R1_005.fastq
lane7_NoIndex_L007_R2_001.fastq
lane7_NoIndex_L007_R2_002.fastq
lane7_NoIndex_L007_R2_003.fastq
lane7_NoIndex_L007_R2_004.fastq
lane7_NoIndex_L007_R2_005.fastq
 
Use iget to download a file to your local system
 
[laureljo@tikal ~/data]$ iget lane7_NoIndex_L007_R1_001.fastq
[laureljo@tikal ~/data]$ ls -l
total 992240
-rw-r--r-x 1 laureljo laureljo 1016048303 Nov 15 13:55 lane7_NoIndex_L007_R1_001.fastq
Use iget -r to download a directory
 
[laureljo@tikal ~/data]$ ils
/BCFZone/home/laureljo:
C- /BCFZone/home/laureljo/110714_L007
C- /BCFZone/home/laureljo/110714_L008
[laureljo@tikal ~/data]$ iget -r 110714_L007
[laureljo@tikal ~/data]$ ls -l
total 4
drwxr-x--- 2 laureljo laureljo 4096 Nov 15 14:07 110714_L007
 
Note: Type iget -h to get a full list of options.
 
 
Reliability Tips and Tricks
If you are having problems with reliability, you can try the following
command options:
 
iget -P -V -T -X <checkpoint-file>