Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Update READEME.md #649

Open
wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Update READEME.md #649

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
e83035e
Update README.md
huoww07 Oct 27, 2022
20c3a0f
Merge pull request #1 from huoww07/huoww07-patch-1
huoww07 Oct 27, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
13 changes: 12 additions & 1 deletion README.md
View file
Open in desktop
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
Expand Down