Singularity with grid engine

JW may 2019

Followed guide here: https://blogs.univa.com/2019/01/using-univa-grid-engine-with-singularity/

Pete installed singularity on phylo

now a request-able resource with "-l singularity" to make sure you get a node with singularity on

Full singularity documentation is here; https://blogs.univa.com/2019/01/using-univa-grid-engine-with-singularity/

Example:

qsub -l singularity -b y singularity run /full_path_to/ubuntu.sif ./test_script.sh
replace: ubuntu.sif with whatever image you are trying to run

Lets go through that command in more depth:

qsub -l singularity -b y singularity run

this is a special command so singularity will run on a specific server

 /full_path_to/ubuntu.sif 

this is the image you download for the software you are interested in

 ./test_script.sh
this needs to contain the commands you want to run

example 2:

qsub -pe multi 8 -l singularity -b y singularity run /full_path/funannotate_latest.sif /full_path/fun_singularity.sh

The shell must have the current working directory full path in it as cd /ful_path/

putting #!cwd command in your shell scripts will not work!
cd /ful_path/
-pe multi 8     this asks for 8 cores, just as normal. 

To add another node with singularity on:

qconf -me <nodename>

On the complex_values line remove NONE if present, and add "singularity=TRUE"