https://github.com/ibchgenomic/hpc-apptainer
apptainer for HPC genome, phylogenomics and evolutionary analysis
https://github.com/ibchgenomic/hpc-apptainer
apptainer apptainer-container devops devops-platform devops-team high-performance-computing phylogenomics phylogenomics-bioinformatics
Last synced: 4 months ago
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apptainer for HPC genome, phylogenomics and evolutionary analysis
- Host: GitHub
- URL: https://github.com/ibchgenomic/hpc-apptainer
- Owner: IBCHgenomic
- License: mit
- Created: 2024-09-30T20:26:28.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2025-02-25T20:16:51.000Z (7 months ago)
- Last Synced: 2025-04-28T07:45:36.144Z (5 months ago)
- Topics: apptainer, apptainer-container, devops, devops-platform, devops-team, high-performance-computing, phylogenomics, phylogenomics-bioinformatics
- Language: Shell
- Homepage:
- Size: 25.4 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# HPC-apptainer
## Multiple apptainer images for HPC computing.
- a apptainer for the phylogenomics. it contains all the applications combined in a single container for the phylogenomics. it incldues orthofinder, astral, trimal, alignmentGO, raxml and clipkit. all the applications required for the genome analysis and genome or gene based phylogenomics.
```
apptainer exec phylogenomics.def
Given an folder of the fasta file you can invoke the apptainer as
apptainer run phylogenomics.sif orthofinder PATH-FASTA-FOLDER
apptainer run phylogenomics.sif astral -h
apptainer run phylogenomics.sif trimal -h
apptainer run phylogenomics.sif alignmentGO -h
apptainer run clipkit -h
```
- post genome assembly apptainer. genome completeness, phylogenomic profiling search. protein-genome alignment for genome annotation inclduing the hint search.
```
apptainer build genomeannotate.sif genomeannotate.def
```
- apptainer for the genome assembly coming from the pacbiohifi reads. it includes two genome assembler and one is hifiasm and the other is verkko. The benchmark for the assembly for these assemblers are located at my another repository [genomeasembly-pacbiohifi](https://github.com/sciencegenome/genomeassembly-pacbiohifi)
- to invoke the hifiasm apptainer
```
module load singularity
apptainer run hifiasm.sif hifiasm
```
- to build and invoke the verkko conda based apptainer. I wrote the verkko yaml so that you can directly import and run with in the apptainer.
```
module load singularity
apptainer build verkko.sif verkko.def
echo ".opt/conda/etc/profile.d/conda.sh" >> $ENV_PATH
```
- inspect the images after the build
```
for i in *.sif; do apptainer inspect ${i}; done
```
- apptainer images for the cpat you can directly call this from the sanbox repositories.
```
apptainer build cpat.sif apptainer.def
```
- to inspect the image
```
apptainer inspect cpat.sif
```
- to run the apptainer image
```
apptainer exec cpat.sif cpat
```
- to run on the computing cluster with the singularity installed
```
module load singularity
```
- to install the apptainer on the new ubuntu version.
```
sh apptainer-install.sh
```
Gaurav Sablok