Merge pull request #1 from uclahs-cds/ts-initial-dev

Migration of RTG-tools Dockerfile to separate repo

.github/ISSUE_TEMPLATE/issue_report.md

@@ -1,7 +1,7 @@
 ---
 name: Docker Issue report
 about: Create a report to help us improve our Docker images
-title: "[DOCKER_ISSUE]"
+title: ""
 labels: ''
 assignees: ''
 

CHANGELOG.md

@@ -1,37 +1,12 @@
 # Changelog
-All notable changes to the tool_name Docker file.
+All notable changes to the RTG-tools Docker file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ---
 
-## [Unreleased]
-### Changed
-- Changed something but it is not part of the last release.
-
----
-
-## [1.0.0] - YYYY-MM-DD
+## [3.12] - 2021-05-07
 ### Added
-- For new features.
-- Added item 1.
-
-### Changed
-- For changes in existing functionality.
-- Changed item 1.
-
-### Deprecated
-- For soon-to-be removed features.
-
-### Removed
-- For now removed features.
-- Removed item 1.
-
-### Fixed
-- For any bug fixes.
-- Fixed item 1.
-
-### Security
-- In case of vulnerabilities.
+- Migrated RTG-tools dockerfile to its own repository

Dockerfile

@@ -1,14 +1,14 @@
 FROM blcdsdockerregistry/bl-base:1.0.0 AS builder
 
 # Use conda to install tools and dependencies into /usr/local
-ARG TOOL_VERSION=X.X.X
+ARG RTGTOOLS_VERSION=3.12
 RUN conda create -qy -p /usr/local \
     -c bioconda \
     -c conda-forge \
-    tool_name==${TOOL_VERSION}
+    rtg-tools==${RTGTOOLS_VERSION}
 
 # Deploy the target tools into a base image
 FROM ubuntu:20.04
 COPY --from=builder /usr/local /usr/local
 
-LABEL maintainer="Your Name <YourName@mednet.ucla.edu>"
+LABEL maintainer="Tim Sanders <TSanders@mednet.ucla.edu>"

README.md

@@ -1,25 +1,23 @@
-# docker-tool_name
-Template Repository for the Boutros Lab Dockerfiles based on the bl-base image.
+# docker-RTGtools
+Dockerfile for RTG-tools, "utilities for accurate VCF comparison and manipulation"
 
-The bl-base image is located in the Boutros Lab Docker Hub repo: https://hub.docker.com/repository/docker/blcdsdockerregistry/bl-base
+The image is located in the Boutros Lab Docker Hub repo: https://hub.docker.com/repository/docker/blcdsdockerregistry/rtg-tools
 
 # Documentation
-Docker introduction [here](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Docker+Introduction)
+RTG-tools main website [here](https://www.realtimegenomics.com/products/rtg-tools)
 
-Dockerfile Best Practices [here](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Dockerfile+Best+Practices)
-
-Docker image versioning standard [here](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Docker+image+versioning+standardization)
+RTG-tools documentation [here](https://cdn.rawgit.com/RealTimeGenomics/rtg-tools/master/installer/resources/tools/RTGOperationsManual/index.html)
 
+GitHub repository [here](https://github.com/RealTimeGenomics/rtg-tools)
 
 # Version
 | Tool | Version |
 |------|---------|
-|tool_name| X.X.X|
-|tool_name_2|X.X.X|
+| RTG-tools | 3.12 |
 
 
 ---
 
 ## References
 
-1. Tool specific references can be listed here
+1. https://www.realtimegenomics.com/products/rtg-tools

metadata.yaml

@@ -1,11 +1,11 @@
 ---
 Category: 'docker'
-Description: 'Template Docker repository for tool_name'  # Description of why the repository exists
-Maintainers: ['YourName@mednet.ucla.edu']  # email address of maintainers
-Contributors: ['Your Name']  # Full names of contributors
-Languages: ['bash']  # programming languages used
-Tools: ['tool_name']  # Name of the tool(s) used in the Dockerfile
-Version: ['X.X.X']  # Tool version number
-Purpose of tool: ''  # Description of what this tool does
-Dependencies: ['docker', 'conda', 'bl-base']  # packages, tools that repo needs to run
-References: ''  # is the tool/dependencies published, is there a confluence page
+Description: 'Dockerfile for RTG-tools'
+Maintainers: ['TSanders@mednet.ucla.edu']
+Contributors: ['Timothy Sanders']
+Languages: ['bash']
+Tools: ['RTG-tools']
+Version: ['3.12']
+Purpose of tool: 'utilities for accurate VCF comparison and manipulation'
+Dependencies: ['docker', 'conda', 'bl-base']
+References: 'https://www.realtimegenomics.com/products/rtg-tools'