Merge pull request #1 from uclahs-cds/sfitz-first-release

add qualimap

CHANGELOG.md

@@ -8,38 +8,12 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ---
 
 ## [Unreleased]
-### Changed
-- Update base Ubuntu image version to `v23.04`
-- Update builder image to mambaforge
-- Switch to GitHub Packages registry in `CICD-base.yaml`
-- Update `metadata.yaml` and `PULL_REQUEST_TEMPLATE.md` and replace Docker Hub with GitHub Packages in the template
-- Changed something but it is not part of the last release.
-
-## Added
-- Add `Docker-build-release.yaml`
-- Add `image_name` to `metadata.yaml`
-
----
-
-## [1.0.0] - YYYY-MM-DD
 ### 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.
+## [2.3] - 2024-01-22
 
-### Fixed
-- For any bug fixes.
-- Fixed item 1.
-
-### Security
-- In case of vulnerabilities.
+### Added
+- Repository template from [template-docker](https://github.com/uclahs-cds/template-docker)
+- `Qualimap` from bioconda

Dockerfile

@@ -1,14 +1,14 @@
-ARG MINIFORGE_VERSION=22.9.0-2
+ARG MINIFORGE_VERSION=23.11.0-0
 ARG UBUNTU_VERSION=23.04
 
 FROM condaforge/mambaforge:${MINIFORGE_VERSION} AS builder
 
 # Use mamba to install tools and dependencies into /usr/local
-ARG TOOL_VERSION=X.X.X
+ARG QUALIMAP_VERSION=2.3
 RUN mamba create -qy -p /usr/local \
     -c bioconda \
     -c conda-forge \
-    tool_name==${TOOL_VERSION}
+    qualimap==${QUALIMAP_VERSION}
 
 # Deploy the target tools into a base image
 FROM ubuntu:${UBUNTU_VERSION} AS final
@@ -21,5 +21,5 @@ RUN groupadd -g 500001 bldocker && \
 # Change the default user to bldocker from root
 USER bldocker
 
-LABEL   maintainer="Your Name <YourName@mednet.ucla.edu>" \
-        org.opencontainers.image.source=https://github.com/uclahs-cds/<REPO>
+LABEL   maintainer="Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>" \
+        org.opencontainers.image.source=https://github.com/uclahs-cds/docker-Qualimap

README.md

@@ -1,53 +1,40 @@
-# docker-tool_name
-Template Repository for the Boutros Lab Dockerfiles based on mambaforge base image.
-
-The base image is pulled from https://hub.docker.com/r/condaforge/mambaforge
-
-# Documentation
-Docker introduction [here](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3190419/Docker+Introduction)
-
-Dockerfile Best Practices [here](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3189770/Dockerfile+Best+Practices)
-
-Docker image versioning standard [here](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3188472/Docker+image+versioning+standardization)
-
+# docker-Qualimap
+Dockerfile for Qualimap, a "a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts."
 
 # Version
 | Tool | Version |
 |------|---------|
-|tool_name| X.X.X|
-|tool_name_2|X.X.X|
+| Qualimap | 2.3 |
 
 ---
 
 ## Discussions
 
-- [Issue tracker](<link-to-issues-page>) to report errors and enhancement ideas.
-- Discussions can take place in [docker-<tool> Discussions](<link-to-discussions>)
-- [docker-<tool> pull requests](<link-to-pull-requests>) are also open for discussion
+- [Issue tracker](https://github.com/uclahs-cds/docker-Qualimap/issues) to report errors and enhancement ideas.
+- Discussions can take place in [docker-Qualimap Discussions](https://github.com/uclahs-cds/docker-Qualimap/discussions)
+- [docker-Qualimap pull requests](https://github.com/uclahs-cds/docker-Qualimap/pulls) are also open for discussion
 
 ---
 
 ## Contributors
 
-Please see list of [Contributors](<link-to-contributors-insights>) at GitHub.
+Please see list of [Contributors](https://github.com/uclahs-cds/docker-Qualimap/graphs/contributors) at GitHub.
 
 ---
 
 ## References
 
-1. Tool specific references can be listed here
+1. http://qualimap.conesalab.org/doc_html/index.html
 
 ---
 
 ## License
 
-Author: Name1, Name2
-
-[docker repo name] is licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license.
+Author: Sorel Fitz-Gibbon <[email protected]>
 
-<one line to give the program's name and a brief idea of what it does.>
+docker-Qualimap is licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license.
 
-Copyright (C) 2023 University of California Los Angeles ("Boutros Lab") All rights reserved.
+Copyright (C) 2024 University of California Los Angeles ("Boutros Lab") All rights reserved.
 
 This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
 

metadata.yaml

@@ -1,10 +1,10 @@
 ---
 category: 'docker'
-description: 'Docker repository for tool_name'  # Description of why the repository exists
-maintainers: ['YourName@mednet.ucla.edu']  # email address of maintainers
-languages: ['Dockerfile']  # programming languages used
-tools: ['tool_name']  # Name of the tool(s) used in the Dockerfile
-version: ['X.X.X']  # Tool version number
-purpose: ''  # Description of what this tool does
-references: ''  # is the tool/dependencies published, is there a confluence page
-image_name: ''  # name of the new docker image
+description: 'Docker repository for Qualimap'
+maintainers: ['sfitzgibbon@mednet.ucla.edu']
+languages: ['Dockerfile']
+tools: ['Qualimap']
+version: ['2.3']
+purpose: 'Quality control of alignment sequencing data'
+references: 'http://bioinformatics.oxfordjournals.org/content/early/2015/09/30/bioinformatics.btv566'
+image_name: 'qualimap'