Anvi'o-Sapelo2: Difference between revisions
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Sapelo2 | Sapelo2 | ||
=== Version === | === Version === | ||
4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 | <!--4, 5.1, 5.3, 5.4, 6.1, 7, 7.1--> | ||
8 | |||
===Author / Distributor=== | ===Author / Distributor=== | ||
Please see http://merenlab.org/software/ | Please see http://merenlab.org/software/ | ||
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For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page. | For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page. | ||
*Version 8 is installed as a singularity image at /apps/singularity-images/anvio_8.sif | |||
<!-- | |||
*Version 4 is installed as a singularity image at /apps/singularity-images/anvio-4.simg | *Version 4 is installed as a singularity image at /apps/singularity-images/anvio-4.simg | ||
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*Version 7.1 (revised on 2022/05) is installed as a singularity image at /apps/singularity-images/anvio_7.1_main_0522.sif | *Version 7.1 (revised on 2022/05) is installed as a singularity image at /apps/singularity-images/anvio_7.1_main_0522.sif | ||
*Version 7.1 is installed as a conda environment in /apps/gb/anvio/7.1 | |||
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singularity exec /apps/singularity-images/anvio_7.1_main_0522.sif ls /opt/conda/envs/anvioenv/bin | singularity exec /apps/singularity-images/anvio_7.1_main_0522.sif ls /opt/conda/envs/anvioenv/bin | ||
</pre> | </pre> | ||
--> | |||
To check all the programs included in the singularity image version 8: | |||
<pre class="gcommand"> | |||
singularity exec /apps/singularity-images/anvio_8.sif ls /opt/conda/envs/anvioenv/bin | |||
</pre> | |||
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To check the version of the anvio programs in the singularity image: | To check the version of the anvio programs in the singularity image: | ||
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tRNA-seq database ............................: 2 | tRNA-seq database ............................: 2 | ||
</pre> | </pre> | ||
--> | |||
<!-- | <!-- | ||
To run v. 7.1, please first load the anvio/7.1_conda module and then activate the conda environment. This example first starts an interactive session: | To run v. 7.1, please first load the anvio/7.1_conda module and then activate the conda environment. This example first starts an interactive session: | ||
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Sample job submission script (sub.sh) to run anvi-profile version | Sample job submission script (sub.sh) to run anvi-profile version 8: | ||
<pre class="gscript"> | <pre class="gscript"> | ||
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cd $SLURM_SUBMIT_DIR | cd $SLURM_SUBMIT_DIR | ||
singularity exec /apps/singularity-images/ | singularity exec /apps/singularity-images/anvio_8.sif anvi-profile [options] | ||
</pre> | </pre> | ||
Latest revision as of 16:08, 15 July 2025
Category
Bioinformatics
Program On
Sapelo2
Version
8
Author / Distributor
Please see http://merenlab.org/software/
Description
From http://merenlab.org/software/anvio: "Anvi’o is an open-source, community-driven analysis and visualization platform for ‘omics data.
It brings together many aspects of today’s cutting-edge genomic, metagenomic, metatranscriptomic, pangenomic, and phylogenomic analysis practices to address a wide array of needs."
Running Program
Also refer to Running Jobs on Sapelo2
For more information on Environment Modules on Sapelo2 please see the Lmod page.
- Version 8 is installed as a singularity image at /apps/singularity-images/anvio_8.sif
To check all the programs included in the singularity image version 8:
singularity exec /apps/singularity-images/anvio_8.sif ls /opt/conda/envs/anvioenv/bin
Sample job submission script (sub.sh) to run anvi-profile version 8:
#!/bin/bash #SBATCH --job-name=testanvio # Job name #SBATCH --partition=batch # Partition (queue) name #SBATCH --ntasks=1 # Run on a single CPU #SBATCH --mem=5gb # Job memory request #SBATCH --time=02:00:00 # Time limit hrs:min:sec #SBATCH --output=%x.%j.out # Standard output log #SBATCH --error=%x.%j.err # Standard error log cd $SLURM_SUBMIT_DIR singularity exec /apps/singularity-images/anvio_8.sif anvi-profile [options]
where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well.
Documentation
Please see http://merenlab.org/software/anvio/
Installation
Singularity images built from the docker container provided by the authors. For example:
singularity pull docker://meren/anvio
System
64-bit Linux