HPC iRODS User Guide

Downloading Illumina data with iRODS module on UA-HPC

*For data retrieval to a desktop or laptop computer, use Cyberduck. Visit our Cyberduck download page for instructions. 

To use iRODs from UA HPC, follow these steps, substituting your iRODs login/password:

Enter the following details into corresponding fields-

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

  • Port:  1247

  • iRODS user:  my_iRODS_login

  • iRODS zone:  BCFZone

Those values will be added to your environment file (for use by other iCommands) if the login succeeds.

  • iRODS password:  my_iRODS_password

After successful iRODS login, confirm the iRODs working directory:

-bash-4.1$ ipwd

/BCFZone/home/my_iRODS_login

 

Use the ils command to list your iRODS project files:

-bash-4.1$ ils

  C- /BCFZone/home/my_iRODS_login/160308_SN885_0999_Lane1SideA_Project_XYZ

 

Use the iget command to upload your iRODS files to your HPC account:

-bash-4.1$ mkdir  /extra/myNetID/160308_ Project_XYZ

-bash-4.1$ cd  /extra/myNetID/160308_ Project_XYZ

-bash-4.1$ iget  –VTr  /BCFZone/home/my_iRODS_login/160308_SN885_0999_Lane1SideA_Project_XYZ


icommands Quick Start Examples

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

These sample commands are entered from the command line once icommands have been installed. Read the official iRODS icommand documentationfor a full description ofthese and other commands.  https://irods.org/documentation/
 

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>