Difference between revisions of "Basemount"
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| − | [[Category:Software]][[Category:Biology]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Sequencing]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|basemount}} | |{{#vardefine:app|basemount}} | ||
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<!--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--> | ||
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<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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{{#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, | |
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| + | jdoe@gator~$ mkdir /blue/mygroup/jdoe/mnt/ | ||
| + | jdoe@gator~$ module load basemount | ||
| + | jdoe@gator~$ basemount /blue/mygroup/jdoe/mnt/ | ||
|}} | |}} | ||
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|}} | |}} | ||
<!--Performance--> | <!--Performance--> | ||
| − | {{#if: {{#var: testing}}|==Performance== | + | {{#if: {{#var: testing}}1|==Performance== |
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| + | If you're running into the following error while running BaseMount: <code>fuse: failed to exec fusermount: No such file or directory</code> | ||
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| + | Try running BaseMount on a login node. Currently, the login nodes are the only ones that have FuserMount available. | ||
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|}} | |}} | ||
Latest revision as of 18:50, 10 June 2022
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.
Environment Modules
Run module spider basemount to find out what environment modules are available for this application.
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/
Performance
If you're running into the following error while running BaseMount: fuse: failed to exec fusermount: No such file or directory
Try running BaseMount on a login node. Currently, the login nodes are the only ones that have FuserMount available.