Hello Ben,
you can configure your Galaxy instance to use your cluster in the job_conf.xml file:
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
You can set up your instance to use your cluster by default for all jobs or only for specific jobs.
Here is a part of my job_conf.xml for example:
<plugins> <!-- LOCAL JOBS --> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
<!-- SUN GRID ENGINE --> <plugin id="sge" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/> </plugins>
<handlers default="handlers"> <handler id="handler0" tags="handlers"/> <handler id="handler1" tags="handlers"/> </handlers>
<destinations default="sge_default"> <destination id="local" runner="local"/> <destination id="sge_default" runner="sge"> <param id="nativeSpecification">-r yes -b n -cwd -S /bin/bash -V -pe galaxy 1</param> </destination> <destination id="sge_big" runner="sge"> <param id="nativeSpecification">-r yes -b n -cwd -S /bin/bash -V -pe galaxy 12</param> </destination>
</destinations>
<tools> <tool id="upload1" destination="local"/> <tool id="toolshed.g2.bx.psu.edu/repos/bhaas/trinityrnaseq/trinityrnaseq/0.0.1" destination="sge_big"/> <tool id="mira_assembler" destination="sge_big"/> <tool id="megablast_wrapper" destination="sge_big"/> <tool id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.1.00" destination="sge_big"/> <tool id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.1.00" destination="sge_big"/> <tool id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.00" destination="sge_big"/> <tool id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00" destination="sge_big"/> <tool id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.1.00" destination="sge_big"/> <tool id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpstblastn_wrapper/0.1.00" destination="sge_big"/> <tool id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.1.00" destination="sge_big"/> </tools>
Moreover you Galaxy user and Galaxy server must be allowed to submit jobs to your scheduler.
Hope it helps,
Thomas