BaseMount

BaseMount is a tool to mount your BaseSpace Sequence Hub data as a Linux file system. You can navigate through projects, samples, runs and app results and interact directly with the associated files exactly as you would with any other local file system. BaseMount is based on FUSE and uses the BaseSpace Sequence Hub API to populate the contents of each directory.

You will need an Illumina BaseSpace account set up before attempting this. BaseMount is installed on all standalones, and the cluster head nodes, but not on cluster nodes.

First create a mount point (an empty directory)

benji@petunia ~ $ mkdir BaseSpace

The first time you mount the BaseSpace file system, you will need to authenticate

benji@petunia ~ $ basemount BaseSpace/
,-----.                        ,--.   ,--.                         ,--.   
|  |) /_  ,--,--. ,---.  ,---. |   `.'   | ,---. ,--.,--.,--,--, ,-'  '-. 
|  .-.  \' ,-.  |(  .-' | .-. :|  |'.'|  || .-. ||  ||  ||      \'-.  .-'
|  '--' /\ '-'  |.-'  `)\   --.|  |   |  |' '-' ''  ''  '|  ||  |  |  |  
`------'  `--`--'`----'  `----'`--'   `--' `---'  `----' `--''--'  `--' 
Illumina BaseMount v0.13.3.1573 public  2016-05-13 14:34

Command called:
    basemount BaseSpace/
From:
    /mnt/lfs2/benji

Starting authentication.

You need to authenticate by opening this URL in a browser:
  https://basespace.illumina.com/oauth/device?code=******
.......
It worked!
Enter new passphrase for access token encryption (optional, press Return to skip): 
Enter same passphrase again: 
Your identification has been saved with the new passphrase.

Mounting BaseSpace account.
To unmount, run: basemount --unmount /mnt/lfs2/benji/BaseSpace

Now you can browse the BaseSpace data as if it were local

benji@petunia ~ $ ls BaseSpace/
Projects  README  Runs
benji@petunia ~ $ ls BaseSpace/Projects/
BaseSpaceDemo  ResequencingPhixRun
benji@petunia ~ $ ls BaseSpace/Runs
20131121_JesseBrunnerAndrewStorfer38  20140319_Anahi_ddRAD  2x151PhiX  BacillusCereus

When you’re done - unmount

benji@petunia ~ $ basemount --unmount /mnt/lfs2/benji/BaseSpace
,-----.                        ,--.   ,--.                         ,--.   
|  |) /_  ,--,--. ,---.  ,---. |   `.'   | ,---. ,--.,--.,--,--, ,-'  '-. 
|  .-.  \' ,-.  |(  .-' | .-. :|  |'.'|  || .-. ||  ||  ||      \'-.  .-'
|  '--' /\ '-'  |.-'  `)\   --.|  |   |  |' '-' ''  ''  '|  ||  |  |  |  
`------'  `--`--'`----'  `----'`--'   `--' `---'  `----' `--''--'  `--' 
Illumina BaseMount v0.13.3.1573 public  2016-05-13 14:34

Command called:
    basemount --unmount /mnt/lfs2/benji/BaseSpace
From:
    /mnt/lfs2/benji

* Soft unmounting of /mnt/lfs2/benji/BaseSpace
Launching: fusermount -u /mnt/lfs2/benji/BaseSpace

/mnt/lfs2/benji/BaseSpace was succesfully unmounted.

See also Illumina’s documentation