https://github.com/romunov/obitools

Docker for OBITools
https://github.com/romunov/obitools

Last synced: 1 day ago
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Docker for OBITools

• Host: GitHub
• URL: https://github.com/romunov/obitools
• Owner: romunov
• Created: 2019-06-14T18:57:28.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2019-06-23T18:13:06.000Z (over 5 years ago)
• Last Synced: 2023-10-20T22:53:29.811Z (about 1 year ago)
• Language: Jupyter Notebook
• Size: 4.88 KB
• Stars: 0
• Watchers: 0
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
This docker wraps [OBITools (1.2.13)](https://git.metabarcoding.org/obitools/obitools/wikis/home) to make the workflows a bit more portable.

The following approach calls obitools functions from Python:

```

import docker

from docker.errors import NotFound

client = docker.from_env()

# Create or start docker container named 'obitools'.

try:

    obt = client.containers.get('obitools')

    if obt.status == 'exited':

        print('Starting container obitools.')

        obt.start()

    else:

        print('Container obitools ready.')

except NotFound:

    print('Creating container obitools.')

    obt = client.containers.run(

        image='romunov/obitools:1.2.13',

        name='obitools',

        # This maps my local wolfdata to /data in container

        volumes={'/home/romunov/wolfdata': {'bind': '/data', 'mode': 'rw'}},

        tty=True, detach=True

        )

```

To run the first command from the [wolves tutorial](https://pythonhosted.org/OBITools/wolves.html#recover-full-sequence-reads-from-forward-and-reverse-partial-reads), you would run something along the lines of

```

reads_r = "wolf_R.fastq"

reads_f = "wolf_F.fastq"

output = "wolf.fastq"

wolf = obt.exec_run(tty=True, workdir='/data', cmd=f'illuminapairedend --score-min={score_min} -r {reads_r} {reads_f} > {output}')

```

The result would be found in `/home/romunov/wolfdata`. See the [vignette Python notebook](vignette_wolf_data.ipynb) for the full workflow.