Anvi'o-Sapelo2 - Revision history

Shtsai at 14:04, 30 March 2026

2026-03-30T14:04:16Z

← Older revision		Revision as of 10:04, 30 March 2026
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	[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==
	Bioinformatics		Bioinformatics
	=== Program On ===		== Program On ==
	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		8
	===Author / Distributor===		==Author / Distributor==
	Please see http://merenlab.org/software/		Please see http://merenlab.org/software/
	===Description===		==Description==
	From http://merenlab.org/software/anvio: "Anvi’o is an open-source, community-driven analysis and visualization platform for ‘omics data.		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."		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 ===		== Running Program ==

	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]
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	</pre>		</pre>
	-->		-->
	=== Documentation ===		== Documentation ==

	Please see http://merenlab.org/software/anvio/		Please see http://merenlab.org/software/anvio/

	=== Installation ===		== Installation ==

	Singularity images built from the docker container provided by the authors. For example:		Singularity images built from the docker container provided by the authors. For example:
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	<!-- The conda environment for v. 7.1 was installed using Miniconda3/4.10.3 and Python 3.6. -->		<!-- The conda environment for v. 7.1 was installed using Miniconda3/4.10.3 and Python 3.6. -->

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Chelsea at 20:08, 15 July 2025

2025-07-15T20:08:02Z

← Older revision		Revision as of 16:08, 15 July 2025
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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 ~~-->~~		*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>

			<!--
	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 ~~7.1_main_0522~~:		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/~~anvio_7.1_main_0522~~.sif anvi-profile [options]		singularity exec /apps/singularity-images/anvio_8.sif anvi-profile [options]

	</pre>		</pre>

Shtsai at 13:23, 1 September 2024

2024-09-01T13:23:50Z

← Older revision		Revision as of 09:23, 1 September 2024
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	*Version 7 is installed as a singularity image at /apps/singularity-images/anvio-7.simg		*Version 7 is installed as a singularity image at /apps/singularity-images/anvio-7.simg

	*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 -->		<!-- *Version 7.1 is installed as a conda environment in /apps/gb/anvio/7.1 -->
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	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	singularity exec /apps/singularity-images/~~anvio-7~~.1_main_0522.sif anvi-profile [options]		singularity exec /apps/singularity-images/anvio_7.1_main_0522.sif anvi-profile [options]

	</pre>		</pre>

Shtsai at 15:27, 5 September 2023

2023-09-05T15:27:08Z

← Older revision		Revision as of 11:27, 5 September 2023
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	<pre class="gcommand">		<pre class="gcommand">
	singularity exec /~~usr/local~~/singularity-images/anvio-6.1.simg ls /opt/conda/envs/anvioenv/bin		singularity exec /apps/singularity-images/anvio-6.1.simg ls /opt/conda/envs/anvioenv/bin
	</pre>		</pre>

			To check all the programs included in the singularity image version 7.1_main_0522:

			<pre class="gcommand">
			singularity exec /apps/singularity-images/anvio_7.1_main_0522.sif ls /opt/conda/envs/anvioenv/bin
			</pre>

	To check the version of the anvio programs in the singularity image:		To check the version of the anvio programs in the singularity image:

Shtsai at 15:24, 5 September 2023

2023-09-05T15:24:41Z

← Older revision		Revision as of 11:24, 5 September 2023
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	*Version 7 is installed as a singularity image at /apps/singularity-images/anvio-7.simg		*Version 7 is installed as a singularity image at /apps/singularity-images/anvio-7.simg

	*Version 7.1 is installed as a conda environment in /apps/gb/anvio/7.1		*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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	</pre>		</pre>

			<pre class="gcommand">
			singularity exec anvio_7.1_main_0522.sif anvi-profile --version
			Anvi'o .......................................: hope (v7.1-dev)
			Profile database .............................: 38
			Contigs database .............................: 20
			Pan database .................................: 15
			Genome data storage ..........................: 7
			Auxiliary data storage .......................: 2
			Structure database ...........................: 2
			Metabolic modules database ...................: 4
			tRNA-seq database ............................: 2
			</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:
	<pre class="gcommand">		<pre class="gcommand">
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	[shtsai@b1-24 ~]$		[shtsai@b1-24 ~]$
	</pre>		</pre>
			-->

			Sample job submission script (sub.sh) to run anvi-profile version 7.1_main_0522:
	Sample job submission script (sub.sh) to run anvi-profile version 6.1:

	<pre class="gscript">		<pre class="gscript">
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	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	singularity exec /apps/singularity-images/anvio-6.1.~~simg~~ anvi-profile [options]		singularity exec /apps/singularity-images/anvio-7.1_main_0522.sif anvi-profile [options]

	</pre>		</pre>
	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.		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.

			<!--
	Sample job submission script (sub.sh) to run anvi-profile version 7.1:		Sample job submission script (sub.sh) to run anvi-profile version 7.1:

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	sbatch sub.sh		sbatch sub.sh
	</pre>		</pre>
			-->
	=== Documentation ===		=== Documentation ===

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	singularity pull docker://meren/anvio		singularity pull docker://meren/anvio

	The conda environment for v. 7.1 was installed using Miniconda3/4.10.3 and Python 3.6.		<!-- The conda environment for v. 7.1 was installed using Miniconda3/4.10.3 and Python 3.6. -->

	=== System ===		=== System ===
	64-bit Linux		64-bit Linux

Shtsai: Created page with "Category:Sapelo2Category:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1..."

2022-01-06T16:02:29Z

Created page with "Category:Sapelo2 Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1..."

New page

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===
Bioinformatics
=== Program On ===
Sapelo2
=== Version ===
4, 5.1, 5.3, 5.4, 6.1, 7, 7.1
===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 4 is installed as a singularity image at /apps/singularity-images/anvio-4.simg

*Version 5.1 is installed as a singularity image at /apps/singularity-images/anvio-5.1.simg

*Version 5.3 is installed as a singularity image at /apps/singularity-images/anvio-5.3.simg

*Version 5.4 is installed as a singularity image at /apps/singularity-images/anvio-5.4.simg

*Version 6.1 is installed as a singularity image at /apps/singularity-images/anvio-6.1.simg

*Version 7 is installed as a singularity image at /apps/singularity-images/anvio-7.simg

*Version 7.1 is installed as a conda environment in /apps/gb/anvio/7.1

To check all the programs included in the singularity image version 5.1:

<pre class="gcommand">
singularity exec /apps/singularity-images/anvio-5.1.simg ls /usr/local/bin
</pre>

To check all the programs included in the singularity image version 6.1:

<pre class="gcommand">
singularity exec /usr/local/singularity-images/anvio-6.1.simg ls /opt/conda/envs/anvioenv/bin
</pre>

To check the version of the anvio programs in the singularity image:

<pre class="gcommand">
singularity exec /usr/local/singularity-images/anvio-6.1.simg anvi-profile --version
Anvi'o version ...............................: esther (v6.1)
Profile DB version ...........................: 31
Contigs DB version ...........................: 14
Pan DB version ...............................: 13
Genome data storage version ..................: 6
Auxiliary data storage version ...............: 2
Structure DB version .........................: 1
</pre>

<pre class="gcommand">
singularity exec /apps/singularity-images/anvio-7.simg anvi-profile --version
Anvi'o .......................................: hope (v7)
Profile database .............................: 35
Contigs database .............................: 20
Pan database .................................: 14
Genome data storage ..........................: 7
Auxiliary data storage .......................: 2
Structure database ...........................: 2
Metabolic modules database ...................: 2
tRNA-seq database ............................: 1
</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:
<pre class="gcommand">
[shtsai@ss-sub1 ~] interact

[shtsai@b1-24 ~] ml anvio/7.1_conda

[shtsai@b1-24 ~] source activate $EBROOTANVIO
(/apps/gb/anvio/7.1) [shtsai@b1-24 ~]$ anvi-profile --version
Anvi'o .......................................: hope (v7.1)

Profile database .............................: 38
Contigs database .............................: 20
Pan database .................................: 15
Genome data storage ..........................: 7
Auxiliary data storage .......................: 2
Structure database ...........................: 2
Metabolic modules database ...................: 2
tRNA-seq database ............................: 2

(/apps/gb/anvio/7.1) [shtsai@b1-24 ~]$ conda deactivate
[shtsai@b1-24 ~]$
</pre>

Sample job submission script (sub.sh) to run anvi-profile version 6.1:

<pre class="gscript">
#!/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-6.1.simg anvi-profile [options]

</pre>
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.

Sample job submission script (sub.sh) to run anvi-profile version 7.1:

<pre class="gscript">
#!/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
ml anvio/7.1_conda
source activate $EBROOTANVIO
anvi-profile [options]
conda deactivate
</pre>
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.

Submit the job to the queue with
<pre class="gcommand">
sbatch sub.sh
</pre>

=== 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

The conda environment for v. 7.1 was installed using Miniconda3/4.10.3 and Python 3.6.

=== System ===
64-bit Linux