Sfitz v2.1.2

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,61 +1,61 @@
-<!--- Please read each of the following items and confirm by replacing the [ ] with a [X] --->
-## Checklist 
+# Description
+<!--- Briefly describe the changes included in this pull request and the paths to the test cases below
+ !--- starting with 'Closes #...' if appropriate --->
 
-### Formatting
+### Closes #...
 
-- [ ] 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).
+## Testing Results
 
-- [ ] 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].
+### Docker Image Testing
 
-- [ ] 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.
+- [ ] I have tested the Docker image with the `docker run` command as described below.
 
-### File Updates
+#### Test the Docker image with at least one sample. Verify the new Docker image works using:
 
-- [ ] 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).
+```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 version number/dependencies and added my name to the maintainer list in the `Dockerfile`.
+#### My command: 
 
-- [ ] I have updated the version number/feature changes in the `README.md`.
+```Provide the command you ran here```
 
-<!--- 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 list in the `metadata.yaml`.
+### Test Cases
 
-- [ ] 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.
+- 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] --->
 
-<!---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 additions/changes and have linked the `CHANGELOG.md` in the release. 
+### Formatting
 
-### Docker Hub Auto Build Rules
+- [ ] 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).
 
-- [ ] I have created automated build rules following [this page](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3200420/How+to+set+up+automated+builds+for+Docker+Hub+deprecated) and I have not manually pushed this Docker image to the `blcdsdockerregistry` on [Docker Hub](https://hub.docker.com).
+- [ ] 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].
 
-### Docker Image Testing
+- [ ] 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.
 
-- [ ] I have tested the Docker image with the `docker run` command as described below.
+### File Updates
 
-#### Test the Docker image with at least one sample. Verify the new Docker image works using:
+- [ ] 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).
 
-```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 version number in the `Dockerfile`, `README.md` and `metadata.yaml` files.
 
-#### My command: 
+- [ ] I have updated the dependencies and added my name to the maintainer list in the `Dockerfile`.
 
-```Provide the command you ran here```
+- [ ] I have updated the feature changes in the `README.md` (optional).
 
-## Description
+- [ ] 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.
 
-<!--- Briefly describe the changes included in this pull request
- !--- starting with 'Closes #...' if approriate --->
+### GitHub Packages Auto Build Rules
 
-Closes #...
-
-<!--- Fill out the results section below with the specific test(s) conducted for this docker image.
- !--- Add additional cases as necessary.
- !--- Remove irrelevant points (depending on the docker image being tested.
- !--- Add points as necessary to completely describe the test. --->
-## Testing Results
+- [ ] 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).
 
-- 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 updated the `image_name`** in the `metadata.yaml` which is required by GitHub action to automatically build and push the image.

CHANGELOG.md

@@ -8,6 +8,9 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ---
 
 ## [Unreleased]
+## [2.1.2] - 2024-10-14
+### Changed
+- Update to MuSE v2.1.2
 
 ## [2.0.4] - 2023-11-13
 ### Changed

Dockerfile

@@ -1,7 +1,7 @@
-FROM ubuntu:20.04
+FROM ubuntu:23.04
 
-ARG MUSE_VERSION=2.0.4
-ARG MUSE_SHA512=8342e648d389b7feef04f870c48bcddbbbdfc85e0c5faf261e6bf68e2f48a02be3e3251691004cf7bb0164de25dc1ef8323dbe5eabc040ba54740c034337a997
+ARG MUSE_VERSION=2.1.2
+ARG MUSE_SHA512=49560abc7e14661be08a5d93e25f38c2e6431bf8c99782324c7b336c6b82bbd7e34ecbeb59299c558eb582288518e783e0ee6f7869503f1d4dc57ca3ea0c1223
 ARG DEBIAN_FRONTEND=noninteractive
 
 RUN apt-get update && apt-get install -y --no-install-recommends \

README.md

@@ -12,7 +12,7 @@ MuSE documentation is [here](https://github.com/wwylab/MuSE).
 # Version
 | Tool | Version |
 |------|---------|
-|MuSE| 2.0.4|
+|MuSE| 2.1.2|
 
 
 ---
@@ -32,7 +32,7 @@ Author: Mao Tian, Sorel Fitz-Gibbon
 
 MuSE is a fast and accurate tool to detect somatic point mutations using the Markov substitution model.
 
-Copyright (C) 2022-2023 University of California Los Angeles ("Boutros Lab") All rights reserved.
+Copyright (C) 2022-2024 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

@@ -5,5 +5,5 @@ Maintainers: ['maotian@mednet.ucla.edu']
 Contributors: ['Mao Tian', 'Sorel Fitz-Gibbon']
 Languages: ['Dockerfile']
 Tools: ['MuSE']
-Version: '2.0.4'
+Version: '2.1.2'
 Image_name: 'MuSE'