From e2597d5dd3ccf27f43ee1cd89bc58a21d12f6757 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Wed, 30 Oct 2024 15:33:35 -0700 Subject: [PATCH 1/5] update to v1.0.1 --- CHANGELOG.md | 4 ++++ Dockerfile | 4 ++-- README.md | 4 ++-- metadata.yaml | 2 +- 4 files changed, 9 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 398235d..b087c71 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,10 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm --- +## [1.0.1] 2024-10-30 +### Changed +- Update to bam-readcount v1.0.1 + ## [0.8.0] - 2021-11-02 ### Added - Create dockerfile for bam-readcount 0.8.0. diff --git a/Dockerfile b/Dockerfile index 2180c73..462e146 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,6 @@ FROM ubuntu:20.04 -ARG BAM_READCOUNT_VERSION=0.8.0 -ARG BAM_READCOUNT_SHA512=ef2acdc9e9b581cb0e4ccea51e3cb445394733f9812f68790a171b71d5f2f089f73aa39a62a6ddf372baa174b884f7d1e52f3f2c9a2abb716599fd7832501a97 +ARG BAM_READCOUNT_VERSION=1.0.1 +ARG BAM_READCOUNT_SHA512=f9b1561774a4280d3d14cd069b13a5ccce40b0ae1a1be1859a36ae268f9a7ecb5b281f4fbbc93a3216ed2a16043b82bf3aa1e418b11c73a6af465048ca524232 RUN apt-get update \ && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends\ build-essential \ diff --git a/README.md b/README.md index 0200b06..48c66ee 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,7 @@ The Boutros lab docker image versioning standard [here](https://confluence.medne # Version | Tool | Version | |------|---------| -|bam-readcount| 0.8.0| +|bam-readcount| 1.0.1| --- @@ -35,7 +35,7 @@ docker-bam-readcount is licensed under the GNU General Public License version 2. docker-bam-readcount is a utility that runs on a BAM or CRAM file and generates low-level information about sequencing data at specific nucleotide positions. -Copyright (C) 2021 University of California Los Angeles ("Boutros Lab") All rights reserved. +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. diff --git a/metadata.yaml b/metadata.yaml index c09e9c6..62fcb36 100644 --- a/metadata.yaml +++ b/metadata.yaml @@ -5,6 +5,6 @@ Maintainers: ['YBugh@mednet.ucla.edu', 'maotian@mednet.ucla.edu'] # email addre Contributors: ['Caden Bugh', 'Mao Tian'] # Full names of contributors Languages: ['Dockerfile'] # programming languages used Tools: ['bam-readcount'] # Name of the tool(s) used in the Dockerfile -Version: ['0.8.0'] # Tool version number +Version: ['1.0.1'] # Tool version number Purpose of tool: 'a utility that counts DNA sequence reads in BAM and CRAM files.' # Description of what this tool does References: 'Khanna, Ajay et al. “Bam-readcount -- rapid generation of basepair-resolution sequence metrics.” ArXiv arXiv:2107.12817v1. 27 Jul. 2021 Preprint.' # is the tool/dependencies published, is there a confluence page From 1097c22500f078892da2d2047824e27e08a292cd Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Wed, 30 Oct 2024 15:39:21 -0700 Subject: [PATCH 2/5] update PR template --- .github/PULL_REQUEST_TEMPLATE.md | 73 +++++++++++++++++--------------- 1 file changed, 39 insertions(+), 34 deletions(-) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 268bd97..5f12f44 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,56 +1,61 @@ -## Description +# Description + - +### Closes #... - -## Checklist +## Testing Results -### Formatting +### Docker Image Testing -- [ ] I have read the [code review guidelines](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Code+Review+Guidelines) and the [code review best practice on GitHub check-list](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Code+Review+Best+Practice+on+GitHub+-+Check+List). +- [ ] I have tested the Docker image with the `docker run` command as described below. -- [ ] The name of the branch is meaningful and well formatted following the [standards](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/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]. +#### Test the Docker image with at least one sample. Verify the new Docker image works using: -- [ ] I have set up or verified the branch protection rule following the [github standards](https://confluence.mednet.ucla.edu/pages/viewpage.action?spaceKey=BOUTROSLAB&title=GitHub+Standards#GitHubStandards-Branchprotectionrule) before opening this pull request. +```docker run -u $(id -u):$(id -g) –w -v : --rm ``` -### File Updates +#### My command: -- [ ] I have updated the version number/dependencies and added my name to the maintainer listing in the `Dockerfile`. +```Provide the command you ran here``` -- [ ] I have updated the version number/feature changes in the `README.md`. +### Test Cases - -- [ ] I have updated the version number and added my name to the contributors listing in the `metadata.yaml`. +- Case 1 + - sample: + - input csv: + - config: + - output: +- Case 2 + - sample: + - input csv: + - config: + - output: + +# Checklist + -- [ ] 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. +### Formatting - -- [ ] I have drafted the new version release with any addidtions/changes and have linked the `CHANGELOG.md` in the release. +- [ ] 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). -### Docker Hub Auto Build Rules +- [ ] 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 created automated build rules following [this page](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/How+to+set+up+automated+builds+for+Docker+Hub) and I have not manually pushed this Docker image to the `blcdsdockerregistry` on [Docker Hub](https://hub.docker.com). +- [ ] 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. -### Docker Image Testing +### File Updates -- [ ] I have tested the Docker image with the `docker run` command as described below. +- [ ] 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). -Test the Docker image with at least one A-mini sample. Verify the new Docker image works using: +- [ ] I have updated the version number in the `Dockerfile`, `README.md` and `metadata.yaml` files. -```docker run -u $(id -u):$(id -g) –w -v : --rm ``` +- [ ] I have updated the dependencies and added my name to the maintainer list in the `Dockerfile`. -My command: +- [ ] I have updated the feature changes in the `README.md` (optional). -```Provide the command you ran here``` - - - -## Testing Results +- [ ] 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. -Closes # +### GitHub Packages Auto Build Rules -- Case 1 - - sample: - - input files: - - config: - - output: +- [ ] 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. From 2d83f4e697edc91bf2d2301a0ffd44259b0e9232 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Wed, 30 Oct 2024 15:44:24 -0700 Subject: [PATCH 3/5] add image_name for auto build --- metadata.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/metadata.yaml b/metadata.yaml index 62fcb36..64a78cd 100644 --- a/metadata.yaml +++ b/metadata.yaml @@ -1,10 +1,11 @@ --- Category: 'docker' Description: 'Docker repository for bam-readcount' # Description of why the repository exists -Maintainers: ['YBugh@mednet.ucla.edu', 'maotian@mednet.ucla.edu'] # email address of maintainers +Maintainers: ['YBugh@mednet.ucla.edu', 'maotian@mednet.ucla.edu','sfitzgibbon@mednet.ucla.edu'] # email address of maintainers Contributors: ['Caden Bugh', 'Mao Tian'] # Full names of contributors Languages: ['Dockerfile'] # programming languages used Tools: ['bam-readcount'] # Name of the tool(s) used in the Dockerfile Version: ['1.0.1'] # Tool version number Purpose of tool: 'a utility that counts DNA sequence reads in BAM and CRAM files.' # Description of what this tool does References: 'Khanna, Ajay et al. “Bam-readcount -- rapid generation of basepair-resolution sequence metrics.” ArXiv arXiv:2107.12817v1. 27 Jul. 2021 Preprint.' # is the tool/dependencies published, is there a confluence page +image_name: 'bam_readcount' From 81cc3e47c9ed2e4c95c9d027e786b8018af5881f Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Wed, 30 Oct 2024 16:37:52 -0700 Subject: [PATCH 4/5] update readme --- README.md | 8 +++----- metadata.yaml | 2 +- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 48c66ee..5b5e48e 100644 --- a/README.md +++ b/README.md @@ -6,12 +6,10 @@ Example: bam-readcount -f ref.fa some.bam ``` The output of bam-readcount is a no header tab-separated file end with `.readcount`. For more description of bam-readcount usage and output, please see [the main github page of bam-readcount](https://github.com/genome/bam-readcount). -The bam-readcount image is located in the Boutros Lab Docker Hub repo [here](https://hub.docker.com/repository/docker/blcdsdockerregistry/bam-readcount). +This image can be found in docker-bam-readcount's GitHub page [here](https://github.com/uclahs-cds/docker-bam-readcount) # Documentation -The main github page of bam-readcount can be found [here](https://github.com/genome/bam-readcount) with documentations. The official latest docker image is available [here](https://hub.docker.com/r/mgibio/bam-readcount). - -The Boutros lab docker image versioning standard [here](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Docker+image+versioning+standardization). +The main github page of bam-readcount can be found [here](https://github.com/genome/bam-readcount) with documentations. # Version @@ -29,7 +27,7 @@ The Boutros lab docker image versioning standard [here](https://confluence.medne ## License -Author: Caden Bugh, Mao Tian +Author: Caden Bugh, Mao Tian, Sorel Fitz-Gibbon docker-bam-readcount is licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license. diff --git a/metadata.yaml b/metadata.yaml index 64a78cd..f8c89c1 100644 --- a/metadata.yaml +++ b/metadata.yaml @@ -1,7 +1,7 @@ --- Category: 'docker' Description: 'Docker repository for bam-readcount' # Description of why the repository exists -Maintainers: ['YBugh@mednet.ucla.edu', 'maotian@mednet.ucla.edu','sfitzgibbon@mednet.ucla.edu'] # email address of maintainers +Maintainers: ['YBugh@mednet.ucla.edu', 'maotian@mednet.ucla.edu', 'sfitzgibbon@mednet.ucla.edu'] # email address of maintainers Contributors: ['Caden Bugh', 'Mao Tian'] # Full names of contributors Languages: ['Dockerfile'] # programming languages used Tools: ['bam-readcount'] # Name of the tool(s) used in the Dockerfile From f33ebbbaa592895e8b6e70900d57dda21b0b314b Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Thu, 31 Oct 2024 12:16:28 -0700 Subject: [PATCH 5/5] add docker-build-release.yaml --- .github/workflows/docker-build-release.yaml | 36 +++++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 .github/workflows/docker-build-release.yaml diff --git a/.github/workflows/docker-build-release.yaml b/.github/workflows/docker-build-release.yaml new file mode 100644 index 0000000..40ae5da --- /dev/null +++ b/.github/workflows/docker-build-release.yaml @@ -0,0 +1,36 @@ +--- +name: Update image in GHCR + +run-name: > + ${{ + github.event_name == 'delete' && format( + 'Delete `{0}{1}`', + github.event.ref_type == 'branch' && 'branch-' || '', + github.event.ref + ) + || github.ref == 'refs/heads/main' && 'Update `dev`' + || format( + 'Update `{0}{1}`', + !startsWith(github.ref, 'refs/tags') && 'branch-' || '', + github.ref_name + ) + }} docker tag + +on: + push: + branches-ignore: ['gh-pages'] + tags: ['v*'] + delete: + +jobs: + push-or-delete-image: + runs-on: ubuntu-latest + name: Update GitHub Container Registry + permissions: + contents: read + packages: write + steps: + - uses: uclahs-cds/tool-Docker-action@v2.1.0 + # Uncomment if you expect to use non-SemVer release tags + # with: + # non-semver-tags: true