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