From 76da2e9c3630868befb75238c6356ebe13407d73 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Sun, 21 Jan 2024 15:07:21 -0800 Subject: [PATCH 1/3] add qualimap --- CHANGELOG.md | 34 ++-------------------------------- Dockerfile | 10 +++++----- README.md | 35 +++++++++++------------------------ metadata.yaml | 16 ++++++++-------- 4 files changed, 26 insertions(+), 69 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a6e5d2c..dc3d64c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,37 +9,7 @@ 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. - -### Fixed -- For any bug fixes. -- Fixed item 1. - -### Security -- In case of vulnerabilities. +- Repository template from [template-docker](https://github.com/uclahs-cds/template-docker) +- Qualimap from bioconda diff --git a/Dockerfile b/Dockerfile index 066ba4d..4afd583 100644 --- a/Dockerfile +++ b/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 " \ - org.opencontainers.image.source=https://github.com/uclahs-cds/ +LABEL maintainer="Sorel Fitz-Gibbon " \ + org.opencontainers.image.source=https://github.com/uclahs-cds/docker-Qualimap diff --git a/README.md b/README.md index 65e9c40..87ae0d2 100644 --- a/README.md +++ b/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]() to report errors and enhancement ideas. -- Discussions can take place in [docker- Discussions]() -- [docker- 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]() at GitHub. +Please see list of [Contributors](https://github.com/uclahs-cds/docker-Qualimap/blob/main/link-to-contributors-insights) 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 - +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. diff --git a/metadata.yaml b/metadata.yaml index 8e06aac..9c1d44a 100644 --- a/metadata.yaml +++ b/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' From de659126d3f49eac9e5d7cb209df09cf54a791f2 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Mon, 22 Jan 2024 10:52:24 -0800 Subject: [PATCH 2/3] typos and fixed link --- CHANGELOG.md | 2 +- README.md | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index dc3d64c..66999fd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,4 +12,4 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm ## Added - Repository template from [template-docker](https://github.com/uclahs-cds/template-docker) -- Qualimap from bioconda +- `Qualimap` from bioconda diff --git a/README.md b/README.md index 87ae0d2..0e38f52 100644 --- a/README.md +++ b/README.md @@ -11,14 +11,14 @@ Dockerfile for Qualimap, a "a platform-independent application written in Java a ## Discussions - [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 +- 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](https://github.com/uclahs-cds/docker-Qualimap/blob/main/link-to-contributors-insights) at GitHub. +Please see list of [Contributors](https://github.com/uclahs-cds/docker-Qualimap/graphs/contributors) at GitHub. --- From c0586b4057000fcde96f413b5ea849f694702758 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Mon, 22 Jan 2024 11:16:58 -0800 Subject: [PATCH 3/3] updated changelog for release --- CHANGELOG.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 66999fd..5320a01 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,8 +8,12 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm --- ## [Unreleased] +### Added + ### Changed -## Added +## [2.3] - 2024-01-22 + +### Added - Repository template from [template-docker](https://github.com/uclahs-cds/template-docker) - `Qualimap` from bioconda