Difference between revisions of "Basemount"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) m (Text replacement - "/ufrc" to "/blue") |
|||
| (4 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
| − | [[Category:Software]][[Category:Biology]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Bioinformatics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|basemount}} | |{{#vardefine:app|basemount}} | ||
| Line 5: | Line 5: | ||
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
| Line 35: | Line 35: | ||
--> | --> | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
| Line 43: | Line 43: | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | ;Note: Create a mount point for basemount within your /blue 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 /blue/mygroup/jdoe/mnt/ | ||
| + | jdoe@gator~$ module load basemount | ||
| + | jdoe@gator~$ basemount /blue/mygroup/jdoe/mnt/ | ||
|}} | |}} | ||
Revision as of 19:22, 11 February 2021
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_BASEMOUNT_DIR - installation directory
Additional Information
- Note
- Create a mount point for basemount within your /blue 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 /blue/mygroup/jdoe/mnt/
jdoe@gator~$ module load basemount
jdoe@gator~$ basemount /blue/mygroup/jdoe/mnt/