Merge pull request #2 from uclahs-cds/mmootor-standardize-repo

Standardize Repo

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,61 @@
+# Description
+<!--- Briefly describe the changes included in this pull request and the paths to the test cases below
+ !--- starting with 'Closes #...' if appropriate --->
+
+### Closes #...
+
+## Testing Results
+
+### Docker Image Testing
+
+- [ ] I have tested the Docker image with the `docker run` command as described below.
+
+#### Test the Docker image with at least one sample. Verify the new Docker image works using:
+
+```docker run -u $(id -u):$(id -g) –w <working-directory> -v <directory-you-want-to-mount>:<how-you-want-to-mount-it-within-the-docker> --rm <docker-image-name> <command-to-the-docker-with-all-parameters>```
+
+#### My command:
+
+```Provide the command you ran here```
+
+### Test Cases
+
+- Case 1
+    - sample:    <!-- e.g. A-mini S2.T-1, A-mini S2.T-n1 -->
+    - input csv: <!-- path/to/input.csv -->
+    - config:    <!-- path/to/xxx.config -->
+    - output:    <!-- path/to/output -->
+- Case 2
+    - sample:    <!-- e.g. A-mini S2.T-1, A-mini S2.T-n1 -->
+    - input csv: <!-- path/to/input.csv -->
+    - config:    <!-- path/to/xxx.config -->
+    - output:    <!-- path/to/output -->
+
+# Checklist
+<!--- Please read each of the following items and confirm by replacing the [ ] with a [X] --->
+
+### Formatting
+
+- [ ] I have read the [code review guidelines](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3187646/Code+Review+Guidelines) and the [code review best practice on GitHub check-list](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3189956/Code+Review+Best+Practice+on+GitHub+-+Check+List).
+
+- [ ] The name of the branch is meaningful and well formatted following the [standards](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3189956/Code+Review+Best+Practice+on+GitHub+-+Check+List), using \[AD_username (or 5 letters of AD if AD is too long)]-\[brief_description_of_branch].
+
+- [ ] I have set up or verified the branch protection rule following the [github standards](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3190380/GitHub+Standards#GitHubStandards-Branchprotectionrule) before opening this pull request.
+
+### File Updates
+
+- [ ] I have ensured that the version number update follows the [versioning standards](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3188472/Docker+image+versioning+standardization).
+
+- [ ] I have updated the version number in the `Dockerfile`, `README.md` and `metadata.yaml` files.
+
+- [ ] I have updated the dependencies and added my name to the maintainer list in the `Dockerfile`.
+
+- [ ] I have updated the feature changes in the `README.md` (optional).
+
+- [ ] I have added the changes included in this pull request to the `CHANGELOG.md` under the next release version or unreleased, and updated the date.
+
+### GitHub Packages Auto Build Rules
+
+- [ ] I have not manually pushed this Docker image to the uclahs-cds container registry (`ghcr.io/uclahs-cds`) on [GitHub](https://github.com/orgs/uclahs-cds/packages).
+
+- [ ] **I have updated the `image_name`** in the `metadata.yaml` which is required by GitHub action to automatically build and push the image.

.github/workflows/CICD-base.yaml

@@ -21,4 +21,4 @@ jobs:
 
       # Run CICD-base
       - name: CICD-base
-        uses: docker://blcdsdockerregistry/cicd-base:latest
+        uses: docker://ghcr.io/uclahs-cds/cicd-base:latest

.github/workflows/Docker-build-release.yaml

@@ -0,0 +1,20 @@
+---
+on:
+  push:
+    branches: ['main']
+    tags: ['v*']
+  release:
+    types: [published]
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    name: A job to build and push a docker image
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - id: build-push
+        uses: uclahs-cds/tool-Docker-action/build-release@latest
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}

CHANGELOG.md

@@ -7,6 +7,29 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ---
 
+## [Unreleased]
+
+---
+
+## [0.16.0] - 2024-04-18
+### Added
+- Add PR template to repo
+- Add `Docker-build-release.yaml` to repo
+- Add `bldocker` as group and user to Dockerfile
+- Set `bldocker` as default user
+
+### Changed
+- Update CICD-base docker registry to `ghcr.io/uclahs-cds`
+- Standardize `README.md`
+- Standardize `metadata.yaml`
+- Standardize Dockerfile
+- Use condaforge as builder
+
+### Removed
+- Remove `blcdsdockerregistry/bl-base` as builder
+
+---
+
 ## [0.16.0] - 2021-08-07
 ### Added
 - Dockerfile and documentation for cnv_facets

Dockerfile

@@ -1,10 +1,13 @@
-FROM blcdsdockerregistry/bl-base:1.0.0 AS builder
+ARG MINIFORGE_VERSION=23.3.1-1
+ARG UBUNTU_VERSION=23.04
+
+FROM condaforge/mambaforge:${MINIFORGE_VERSION} AS builder
 
 # Use conda to install tools and dependencies into /usr/local
 ENV CNVFACETS_VERSION=0.16.0 \
     SAMTOOLS_VERSION=1.9 \
     MSCOREFONTS_VERSION=0.0.1
-RUN conda create -qy -p /usr/local \
+RUN mamba create -qy -p /usr/local \
         -c bioconda \
         -c conda-forge \
         cnv_facets==${CNVFACETS_VERSION} \
@@ -15,7 +18,15 @@ RUN conda create -qy -p /usr/local \
 RUN R -e 'install.packages("BiocManager", repos="http://cran.us.r-project.org"); BiocManager::install("GenomeInfoDbData")'
 
 # Deploy the target tools into a base image
-FROM ubuntu:20.04
+FROM ubuntu:${UBUNTU_VERSION} AS final
 COPY --from=builder /usr/local /usr/local
 
-LABEL maintainer="Cyriac Kandoth <[email protected]>"
+# Add a new user/group called bldocker
+RUN groupadd -g 500001 bldocker && \
+    useradd -r -u 500001 -g bldocker bldocker
+
+# Change the default user to bldocker from root
+USER bldocker
+
+LABEL maintainer="Mohammed Faizal Eeman Mootor <[email protected]>" \
+    org.opencontainers.image.source=https://github.com/uclahs-cds/docker-cnv_facets

README.md

@@ -16,7 +16,35 @@ Tips for understanding FACETS results [here](https://bandla-chai.gitbook.io/face
 |cnv_facets|0.16.0|
 ---
 
+## Discussions
+
+- [Issue tracker](https://github.com/uclahs-cds/docker-cnv_facets/issues) to report errors and enhancement ideas.
+- Discussions can take place in [docker-cnv_facets Discussions](https://github.com/uclahs-cds/docker-cnv_facets/discussions)
+- [docker-cnv_facets pull requests](https://github.com/uclahs-cds/docker-cnv_facets/pulls) are also open for discussion
+
+---
+
+## Contributors
+
+Please see list of [Contributors](https://github.com/uclahs-cds/docker-cnv_facets/graphs/contributors) at GitHub.
+
+---
+
 ## References
 1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5027494/
 2. https://github.com/mskcc/facets
 3. https://github.com/dariober/cnv_facets
+
+---
+
+## License
+
+Author: 'Cyriac Kandoth', 'Mohammed Faizal Eeman Mootor'
+
+docker-cnv_facets is licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license.
+
+docker-cnv_facets can be used to create a docker instance to use cnv_facets.
+
+Copyright (C) 2021-2024 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 cnv_facets'
-Maintainers: ['ckandoth@mednet.ucla.edu']
-Contributors: ['Cyriac Kandoth']
-Languages: ['Dockerfile']
-Tools: ['cnv_facets']
-Version: ['0.16.0']
-Purpose of tool: 'Allele-specific somatic copy-number variant caller'
-References: 'https://github.com/dariober/cnv_facets'
+category: 'docker'
+description: 'Docker repository for cnv_facets'
+maintainers: ['mmootor@mednet.ucla.edu']
+languages: ['Dockerfile']
+tools: ['cnv_facets']
+version: ['0.16.0']
+purpose: 'Allele-specific somatic copy-number variant caller'
+references: 'https://github.com/dariober/cnv_facets'
+image_name: 'cnv_facets'