Difference between revisions of "Basemount"

Revision as of 21:33, 9 August 2016

Description

BaseMount is a tool to mount your BaseSpace 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 a FUSE, which operates in user-space and uses the BaseSpace API to populate the contents of each directory.

Required Modules

Serial

basemount

System Variables

HPC_{{#uppercase:basemount}}_DIR - installation directory

Additional Information

Note: Create a mount point for basemount within your /ufrc space to avoid getting a 'permission denied' error as basemount tries to use a system directory /mnt to mount your Illumina Basespace project directory. For example,

jdoe@gator~$ mkdir /ufrc/mygroup/jdoe/mnt/

jdoe@gator~$ module load basemount

jdoe@gator~$ basemount /ufrc/mygroup/jdoe/mnt/

@@ Line 5: / Line 5: @@
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
-|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
+|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 |{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
@@ Line 43: / Line 43: @@
 {{#if: {{#var: exe}}|==Additional Information==
-WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+;Note: Create a mount point for basemount within your /ufrc space to avoid getting a 'permission denied' error as basemount tries to use a system directory /mnt to mount your Illumina Basespace project directory. For example,
+ jdoe@gator~$ mkdir /ufrc/mygroup/jdoe/mnt/
+ jdoe@gator~$ module load basemount
+ jdoe@gator~$ basemount /ufrc/mygroup/jdoe/mnt/
 |}}