Anvi'o-Sapelo2: Difference between revisions
Jump to navigation
Jump to search
(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...") |
No edit summary |
||
| (2 intermediate revisions by the same user not shown) | |||
| Line 30: | Line 30: | ||
*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 --> | |||
| Line 42: | Line 44: | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
singularity exec / | 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: | ||
| Line 72: | Line 79: | ||
</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"> | ||
| Line 94: | Line 115: | ||
[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 | |||
<pre class="gscript"> | <pre class="gscript"> | ||
| Line 110: | Line 131: | ||
cd $SLURM_SUBMIT_DIR | cd $SLURM_SUBMIT_DIR | ||
singularity exec /apps/singularity-images/ | 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: | ||
| Line 140: | Line 161: | ||
sbatch sub.sh | sbatch sub.sh | ||
</pre> | </pre> | ||
--> | |||
=== Documentation === | === Documentation === | ||
| Line 151: | Line 172: | ||
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 | ||
Latest revision as of 08:23, 1 September 2024
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 (revised on 2022/05) is installed as a singularity image at /apps/singularity-images/anvio_7.1_main_0522.sif
To check all the programs included in the singularity image version 5.1:
singularity exec /apps/singularity-images/anvio-5.1.simg ls /usr/local/bin
To check all the programs included in the singularity image version 6.1:
singularity exec /apps/singularity-images/anvio-6.1.simg ls /opt/conda/envs/anvioenv/bin
To check all the programs included in the singularity image version 7.1_main_0522:
singularity exec /apps/singularity-images/anvio_7.1_main_0522.sif ls /opt/conda/envs/anvioenv/bin
To check the version of the anvio programs in the singularity image:
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
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
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
Sample job submission script (sub.sh) to run anvi-profile version 7.1_main_0522:
#!/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_7.1_main_0522.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