Initial commit

.github/ISSUE_TEMPLATE/issue_report.md

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+---
+name: Issue report
+about: Create a report to help us improve our Docker images
+title: ""
+labels: ''
+assignees: ''
+
+---
+
+**Describe the issue**
+A clear and concise description of what the issue is. Please include the following in your issue report along with any explicit errors observed
+* Docker image release version
+* Cluster you are using (SGE/Slurm-Dev/Slurm-Test)
+* Config files (if applicable)
+* Path to the working directory
+* Any logs produced by the pipeline
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Additional context**
+Add any other context about the problem here.

.github/workflows/CICD-base.yaml

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+---
+name: CICD-base
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+jobs:
+  CICD-base:
+    runs-on: ubuntu-latest
+
+    timeout-minutes: 15
+
+    steps:
+      # Checkout codebase
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      # Run CICD-base
+      - name: CICD-base
+        uses: docker://blcdsdockerregistry/cicd-base:latest

.gitignore

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+# System files
+.DS_Store
+
+# R
+.Rhistory
+.Rapp.history
+.Rproj.user
+.RData

CHANGELOG.md

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+# Changelog
+All notable changes to the tool_name 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
+### 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.

Dockerfile

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+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
+RUN conda create -qy -p /usr/local \
+    -c bioconda \
+    -c conda-forge \
+    tool_name==${TOOL_VERSION}
+
+# Deploy the target tools into a base image
+FROM ubuntu:20.04
+COPY --from=builder /usr/local /usr/local
+
+LABEL maintainer="Your Name <[email protected]>"

README.md

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+# docker-tool_name
+Template Repository for the Boutros Lab Dockerfiles based on the bl-base image.
+
+The bl-base image is located in the Boutros Lab Docker Hub repo: https://hub.docker.com/repository/docker/blcdsdockerregistry/bl-base
+
+# Documentation
+Docker introduction [here](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Docker+Introduction)
+
+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)
+
+
+# Version
+| Tool | Version |
+|------|---------|
+|tool_name| X.X.X|
+|tool_name_2|X.X.X|
+
+
+---
+
+## References
+
+1. Tool specific references can be listed here

metadata.yaml

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+---
+Category: 'docker'
+Description: 'Template Docker repository for tool_name'  # Description of why the repository exists
+Maintainers: ['[email protected]']  # email address of maintainers
+Contributors: ['Your Name']  # Full names of contributors
+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 of tool: ''  # Description of what this tool does
+References: ''  # is the tool/dependencies published, is there a confluence page