From f53abc52d36b68412cf14172ddcfc96f166ac880 Mon Sep 17 00:00:00 2001 From: Cyriac Kandoth Date: Thu, 8 Jul 2021 09:58:31 -0700 Subject: [PATCH] Initial commit --- .github/ISSUE_TEMPLATE/issue_report.md | 32 ++++++++++++++++++++++ .github/workflows/CICD-base.yaml | 24 +++++++++++++++++ .gitignore | 8 ++++++ CHANGELOG.md | 37 ++++++++++++++++++++++++++ Dockerfile | 14 ++++++++++ README.md | 25 +++++++++++++++++ metadata.yaml | 10 +++++++ 7 files changed, 150 insertions(+) create mode 100644 .github/ISSUE_TEMPLATE/issue_report.md create mode 100644 .github/workflows/CICD-base.yaml create mode 100644 .gitignore create mode 100644 CHANGELOG.md create mode 100644 Dockerfile create mode 100644 README.md create mode 100644 metadata.yaml diff --git a/.github/ISSUE_TEMPLATE/issue_report.md b/.github/ISSUE_TEMPLATE/issue_report.md new file mode 100644 index 0000000..7bcd9b5 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/issue_report.md @@ -0,0 +1,32 @@ +--- +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. diff --git a/.github/workflows/CICD-base.yaml b/.github/workflows/CICD-base.yaml new file mode 100644 index 0000000..682124b --- /dev/null +++ b/.github/workflows/CICD-base.yaml @@ -0,0 +1,24 @@ +--- +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 diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..e0a1def --- /dev/null +++ b/.gitignore @@ -0,0 +1,8 @@ +# System files +.DS_Store + +# R +.Rhistory +.Rapp.history +.Rproj.user +.RData diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..3daf420 --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,37 @@ +# 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. \ No newline at end of file diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..8f58b10 --- /dev/null +++ b/Dockerfile @@ -0,0 +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 +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 " \ No newline at end of file diff --git a/README.md b/README.md new file mode 100644 index 0000000..d42fbbc --- /dev/null +++ b/README.md @@ -0,0 +1,25 @@ +# 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 \ No newline at end of file diff --git a/metadata.yaml b/metadata.yaml new file mode 100644 index 0000000..9e9ec34 --- /dev/null +++ b/metadata.yaml @@ -0,0 +1,10 @@ +--- +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: ['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