<commit_before>[![DOI](https://zenodo.org/badge/5466/bgruening/docker-galaxy-stable.svg)](https://zenodo.org/badge/latestdoi/5466/bgruening/docker-galaxy-stable)
[![Build Status](https://travis-ci.org/bgruening/docker-galaxy-stable.svg?branch=master)](https://travis-ci.org/bgruening/docker-galaxy-stable)
[![Docker Repository on Quay](https://quay.io/repository/bgruening/galaxy/status "Docker Repository on Quay")](https://quay.io/repository/bgruening/galaxy)
[![Gitter](https://badges.gitter.im/bgruening/docker-galaxy-stable.svg)](https://gitter.im/bgruening/docker-galaxy-stable?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
![docker pulls](https://img.shields.io/docker/pulls/bgruening/galaxy-stable.svg) ![docker stars](https://img.shields.io/docker/stars/bgruening/galaxy-stable.svg)

Galaxy Docker Compose
=====================

# Table of Contents <a name="toc" />

- [Usage](#Usage)
    - [Build](#Build)
    - [Start Container](#Start)
    - [Stop Container](#Stop)
    - [Docker Swarm](#Swarm)
- [Advanced](#Advanced)
  - [postgres](#postgres)
    - [Configuration](#postgres-Configuration)
  - [proftpd](#proftpd)
    - [Configuration](#proftpd-Configuration)
  - [slurm](#slurm)
    - [Configuration](#slurm-Configuration)
  - [galaxy-init](#galaxy-init)
    - [Configuration](#galaxy-init-Configuration)

<p align="right"><a href="#toc">&#x25B2; back to top</a></p>

# Architectural Overview

![Architectural Overview](./galaxy-compose.svg)


# Usage <a name="Usage" />

At first you need to install docker with [compose](https://docs.docker.com/compose).
- [docker](https://docs.docker.com/installation/)
- [docker-compose](https://docs.docker.com/compose/install/)

<p align="right"><a href="#toc">&#x25B2; back to top</a></p>

## Build <a name="Build" />

Clone the repository:
```
git clone https://github.com/bgruening/docker-galaxy-stable.git
cd docker-galaxy-stable/compose
```

Build the compose containers:
```sh
./buildlocal.sh
```

<p align="right"><a href="#toc">&#x25B2; back to top</a></p>

## Start Container <a name="Start" />

After successful installation you can start your composed Galaxy version with:
```sh
docker-compose up -d<commit_msg>update build instructions<commit_after>[![DOI](https://zenodo.org/badge/5466/bgruening/docker-galaxy-stable.svg)](https://zenodo.org/badge/latestdoi/5466/bgruening/docker-galaxy-stable)
[![Build Status](https://travis-ci.org/bgruening/docker-galaxy-stable.svg?branch=master)](https://travis-ci.org/bgruening/docker-galaxy-stable)
[![Docker Repository on Quay](https://quay.io/repository/bgruening/galaxy/status "Docker Repository on Quay")](https://quay.io/repository/bgruening/galaxy)
[![Gitter](https://badges.gitter.im/bgruening/docker-galaxy-stable.svg)](https://gitter.im/bgruening/docker-galaxy-stable?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
![docker pulls](https://img.shields.io/docker/pulls/bgruening/galaxy-stable.svg) ![docker stars](https://img.shields.io/docker/stars/bgruening/galaxy-stable.svg)

Galaxy Docker Compose
=====================

# Table of Contents <a name="toc" />

- [Usage](#Usage)
    - [Build](#Build)
    - [Start Container](#Start)
    - [Stop Container](#Stop)
    - [Docker Swarm](#Swarm)
- [Advanced](#Advanced)
  - [postgres](#postgres)
    - [Configuration](#postgres-Configuration)
  - [proftpd](#proftpd)
    - [Configuration](#proftpd-Configuration)
  - [slurm](#slurm)
    - [Configuration](#slurm-Configuration)
  - [galaxy-init](#galaxy-init)
    - [Configuration](#galaxy-init-Configuration)

<p align="right"><a href="#toc">&#x25B2; back to top</a></p>

# Architectural Overview

![Architectural Overview](./galaxy-compose.svg)


# Usage <a name="Usage" />

At first you need to install docker with [compose](https://docs.docker.com/compose).
- [docker](https://docs.docker.com/installation/)
- [docker-compose](https://docs.docker.com/compose/install/)

<p align="right"><a href="#toc">&#x25B2; back to top</a></p>

## Build <a name="Build" />

Clone the repository:
```
git clone https://github.com/bgruening/docker-galaxy-stable.git
cd docker-galaxy-stable/compose
```

Build the compose containers:
```sh
./build-orchestration-images.sh --no-push --condor --grafana --slurm --k8s
source ./tags-for-compose-to-source.sh
```

<p align="right"><a href="#toc">&#x25B2; back to top</a></p>

## Start Container <a name="Start" />

After successful installation you can start your composed Galaxy version with:
```sh
docker-compose up -d
{'fraction_non_alphanumeric': 0.20062416406598305, 'fraction_numerical': 0.00780205082478823, 'mean_word_length': 5.030913978494624, 'pattern_counts': {'":': 0, '<': 35, '<?xml version=': 0, '>': 35, 'https://': 28, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3170519', 'n_tokens_mistral': 1693, 'n_tokens_neox': 1564, 'n_words': 234}