https://github.com/applicativesystem/genome-assembly-apptainer

multi-sif-apptainer images for genome assembly
https://github.com/applicativesystem/genome-assembly-apptainer

apptainer apptainer-container bioinformatics devops-platform devops-tools genome-assembly hifiasm system-administration verkko

Last synced: 23 days ago
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multi-sif-apptainer images for genome assembly

• Host: GitHub
• URL: https://github.com/applicativesystem/genome-assembly-apptainer
• Owner: applicativesystem
• Created: 2024-09-27T05:44:05.000Z (3 months ago)
• Default Branch: main
• Last Pushed: 2024-10-01T21:29:09.000Z (3 months ago)
• Last Synced: 2024-11-10T20:18:06.512Z (about 2 months ago)
• Topics: apptainer, apptainer-container, bioinformatics, devops-platform, devops-tools, genome-assembly, hifiasm, system-administration, verkko
• Homepage:
• Size: 6.84 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# genome-assembly-pacbiohifi-apptainer

- 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/codecreatede/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

``

Gaurav Sablok