Running Anvi'o on C1

Anvi'o versions 3, 4 and 5 are installed in their own environments within SCGC's anaconda3 package.

To load Anvi'o version 5 type:

module load anaconda3
source activate anvio5

To run it interactively, start an interactive session on charlie like so: (Note that by running "module purge" all other loaded software modules are also unloaded.)

julia at cfe1 in ~
$ qsub -I -q route -l walltime=8:00:00 -l ncpus=5,mem=32G -N anvio-interactive
qsub: waiting for job 33493.cfe1 to start
qsub: job 33493.cfe1 ready

julia at c1 in ~
$ module purge

julia at c1 in ~
$ module load anaconda3

julia at c1 in ~
$ source activate anvio5

From there you should be able to run any of the Anvi'o commands. e.g.:

(anvio5)
julia at c1 in ~
$ anvi-profile --version
Anvi'o version ...............................: 4
Profile DB version ...........................: 23
Contigs DB version ...........................: 10
Pan DB version ...............................: 8
Genome data storage version ..................: 6
Auxiliary data storage version ...............: 2

If you run a job submission using Anvi'o, make sure you have:

module purge
module load anaconda3
source activate anvio5

After your PBS parameters and before your terminal commands.

Click here for instructions on how to interact with your Anvi'o session on C1 through a local browser.