Difference between revisions of "VarSimLab"
Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:BiologyCategory:Genomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|varsimlab}} |{{#vardefine:url|https://github.com/NabaviLab/Va...") |
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| − | [[Category:Software]][[Category:Biology]][[Category:Genomics]] | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:Simulation]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|varsimlab}} | |{{#vardefine:app|varsimlab}} | ||
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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:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==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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Port selection is pseudo-random to avoid port collisions from multiple jobs. Note the printed port number and hostname and use them in the ssh tunnel command: | Port selection is pseudo-random to avoid port collisions from multiple jobs. Note the printed port number and hostname and use them in the ssh tunnel command: | ||
| − | ssh -L 8000:$host:$port $user@ | + | ssh -L 8000:$host:$port $user@hpg.rc.ufl.edu -N |
where $host and $port are the values from the job log and $user is your GatorLink username. | where $host and $port are the values from the job log and $user is your GatorLink username. | ||
| + | |||
| + | You can browse to http://localhost:8000 in the web browser on your local machine after the SSH tunnel is established. | ||
|}} | |}} | ||
Latest revision as of 17:24, 22 August 2022
Description
VarSimLab is a web-based package for studying genomic variations in a given genome. As of the current version (nabavilab/varsimlab:0.2), the simulator generates artificial short reads, which harbor structural and copy number variations. In addition, it simulates tumor heterozygosity (Ploidy and Subclones).
Environment Modules
Run module spider varsimlab to find out what environment modules are available for this application.
System Variables
- HPC_VARSIMLAB_DIR - installation directory
Additional Information
To run the VarSimLab web application in a batch job load the varsimlab module and run
varsimlab
In the job log you'll see something along the lines of
Starting VarSimLab on all network interfaces and port 11736 on some_node.ufhpc Performing system checks...
VarSimLab 1.0: reading manifest.json .. VarSimLab 1.0: found all required simulation files in place; simulation is READY! System check identified no issues (0 silenced). February 20, 2018 - 21:49:37 Django version 1.9.7, using settings 'easyscnvsim.settings' Starting development server at http://0.0.0.0:11736/ Quit the server with CONTROL-C.
Port selection is pseudo-random to avoid port collisions from multiple jobs. Note the printed port number and hostname and use them in the ssh tunnel command:
ssh -L 8000:$host:$port $user@hpg.rc.ufl.edu -N
where $host and $port are the values from the job log and $user is your GatorLink username.
You can browse to http://localhost:8000 in the web browser on your local machine after the SSH tunnel is established.