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Anvi'o
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:
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module load anaconda3
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source activate anvio5
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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.)
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julia at cfe1 in ~
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$ qsub -I -q route -l walltime=8:00:00 -l ncpus=5,mem=32G -N anvio-interactive
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qsub: waiting for job 33493.cfe1 to start
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qsub: job 33493.cfe1 ready
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julia at c1 in ~
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$ module purge
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julia at c1 in ~
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$ module load anaconda3
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julia at c1 in ~
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$ source activate anvio5
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From there you should be able to run any of the Anvi'o commands. e.g.:
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(anvio5)
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julia at c1 in ~
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$ anvi-profile --version
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Anvi'o version ...............................: 4
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Profile DB version ...........................: 23
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Contigs DB version ...........................: 10
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Pan DB version ...............................: 8
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Genome data storage version ..................: 6
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Auxiliary data storage version ...............: 2
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If you run a job submission using Anvi'o, make sure you have:
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module purge
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module load anaconda3
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source activate anvio5
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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.
Last modified 2yr ago
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