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Update READEME.md #649

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Update README.md
huoww07 Oct 27, 2022
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Merge pull request #1 from huoww07/huoww07-patch-1
huoww07 Oct 27, 2022
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13 changes: 12 additions & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -31,15 +31,26 @@ brew install brewsci/bio/prokka
### Docker
Maintained by https://hub.docker.com/u/staphb
```

# pull docker image to local
docker pull staphb/prokka:latest

# test run to print out help messages from prokka
docker run staphb/prokka:latest prokka -h

# actual run: remember to add <absolute path to folder containing contigs.fa> such as /user/Documents
docker run -v <absolute path to folder containing contigs.fa>:/mydata staphb/prokka:latest prokka --outdir /mydata/annotation /mydata/contigs.fa
```

### Singularity
```
# build local image
singularity build prokka.sif docker://staphb/prokka:latest

# test run to print out help messages from prokka
singularity exec prokka.sif prokka -h

# actual run: remember to use --bind to link absolute local path continaing contigs.fa to singularity path /mydata
singularity exec --bind /local/path/to/fasta:/mydata prokka.sif prokka --outdir /mydata/annotation /mydata/contigs.fasta
```

### Ubuntu/Debian/Mint
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