https://github.com/multimeric/dockercli

A command line tool for running executable docker images, and automatically mounting in any files used in the command
https://github.com/multimeric/dockercli

bioinformatics

Last synced: 5 months ago
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A command line tool for running executable docker images, and automatically mounting in any files used in the command

• Host: GitHub
• URL: https://github.com/multimeric/dockercli
• Owner: multimeric
• License: gpl-3.0
• Created: 2018-07-31T02:33:31.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2018-07-31T06:39:18.000Z (over 7 years ago)
• Last Synced: 2025-10-12T13:38:51.393Z (5 months ago)
• Topics: bioinformatics
• Language: Python
• Homepage:
• Size: 78.1 KB
• Stars: 2
• Watchers: 0
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# Docker CLI

`docker-cli` is a command-line tool for running executable docker images, which automatically mounts any necessary

files into the container.

For example, let's say you want to run the command-line tool [`bwa`](http://bio-bwa.sourceforge.net/). If you have

`bwa` installed locally, you could use a command like this. Easy!

```bash

bwa index hg19.fasta

```

However, if you wanted to do this inside a docker container, you would first have to mount the file into the container,

making the command much more complicated and slow to write:

```bash

docker run -v hg19.fasta:/tmp lh3lh3/bwa index /tmp/hg19.fasta

```

`docker-cli` automatically generates these mount flags, allowing you to instead run:

```bash

docker-cli lh3lh3/bwa hg19.fasta

```

## Installation

To install the command, first ensure you have Python 3.6 or above installed. Then, run:

```bash

python3 -m pip install git+https://github.com/TMiguelT/DockerCli

```

## Usage

Once you install this package, you will have the `docker-cli` command available. Use this command exactly as you would

the normal `docker run` command; `docker run --rm mycontainer` becomes `docker-cli mycontainer`.

The full command line interface, including additional flags, is listed here:

```

usage: docker-cli [-h] [-n] [-p] [-e] ...

Runs a Docker image, automatically converting filepaths to a bindmount inside

the container

positional arguments:

  arguments           Arguments to pass to the docker container

optional arguments:

  -h, --help          show this help message and exit

  -n, --no-rm         Don't delete the container after it runs (the default)

  -p, --mount-parent  Mount the containing folder for each file, rather than

                      mounting each file individually. This can be helpful when

                      using index files etc.

  -e, --echo-command  Print the generated docker command instead of running

```