Merge pull request #3 from uclahs-cds/sfitz-v1.0.1

update to v1.0.1

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,56 +1,61 @@
-## Description
+# Description
+<!--- Briefly describe the changes included in this pull request and the paths to the test cases below
+ !--- starting with 'Closes #...' if appropriate --->
 
-<!--Provide a brief summary of the PR here-->
+### Closes #...
 
-<!--- Please read each of the following items and confirm by replacing the [ ] with a [X] --->
-## 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 <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>```
 
-### 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
 
-<!--- This acknowledgement is optional if you do not want to be listed--->
-- [ ] I have updated the version number and added my name to the contributors listing in the `metadata.yaml`.
+- 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] --->
 
-- [ ] 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
 
-<!---If any previous versions have bugs, add "deprecated" in the version tag and list the bug in the corresponding release--->
-- [ ] 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 <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>```
+- [ ] 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```
-
-<!--- Copy and paste the results list below for more cases that were tested--->
-<!--- If the case addresses an issue that should be closed, begin with "Closes <Issue #>"--->
-## 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 #<!--Issue #-->
+### GitHub Packages Auto Build Rules
 
-- Case 1
-    - sample: <!-- e.g. A-mini S2.T-1, A-mini S2.T-n1 -->
-    - input files: <!--path to input file(s) (if more than one, list in indented bullet points below this line)-->
-    - config: <!--path to config file-->
-    - output: <!--path to output directory-->
+- [ ] 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/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

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.

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 \

README.md

@@ -6,18 +6,16 @@ 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
 | Tool | Version |
 |------|---------|
-|bam-readcount| 0.8.0|
+|bam-readcount| 1.0.1|
 
 ---
 
@@ -29,13 +27,13 @@ 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.
 
 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.
 

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: ['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
+image_name: 'bam_readcount'