https://github.com/nci-gdc/vep-tool

bioinformatics docker workflow-tool

Last synced: 2 months ago
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GDC VEP Plugins

Host: GitHub
URL: https://github.com/nci-gdc/vep-tool
Owner: NCI-GDC
License: apache-2.0
Created: 2016-03-31T14:49:17.000Z (about 10 years ago)
Default Branch: master
Last Pushed: 2025-03-10T21:33:15.000Z (over 1 year ago)
Last Synced: 2025-10-06T19:47:07.718Z (9 months ago)
Topics: bioinformatics, docker, workflow-tool
Language: Perl
Homepage:
Size: 58.6 KB
Stars: 0
Watchers: 7
Forks: 1
Open Issues: 2
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Notice: NOTICE

README

Further documentation available [here](https://docs.google.com/document/d/17NFwGvn4vMEXZV9Qmg30BqAcKrdxBYCOB4pFdkkwIIo/edit#)

# Using this template

This template repository should be used as the base for new Dockerized softare repositories.

# Software Dockers of multiple versions

## Pre-requisites

- Docker
- [just](https://github.com/casey/just)

`just init` will install the correct version of `pre-commit`, be sure to have a python3.8+ virtual environment active.

- `just build ` will create the Docker for the specified VERSION

`just build-all` will build all available Docker images.

## Just

The `just` utility is a command runner replacement for `make`.

It has various improvements over `make` including the ability to list available command with `just -l`:

### Root Justfile

```
Available recipes:
build VERSION # Builds individual workflow
build-all # Builds all docker images for each directory with a justfile
init
```

The root `justfile` provides recipes for Dockerizing workflows locally, while workflow-level `justfiles` provide recipes for building the workflow.

### Workflow Justfile

The version-level `justfile` requires the `DOCKERFILE` path be updated.

```
# justfile
DOCKERFILE := "../Dockerfile.multi"
```

Many kinds of software are able to share a single Dockerfile with a parameterized version.

However, if a particular version needs a bespoke Dockerfile, simply create on in the version directory and upate the justfile:

```
# justfile
DOCKERFILE := "./Dockerfile"
```

```
Available recipes:
emit-dockerfile # Prints which Dockerfile to use for CI builds
```