Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Sfitz v2.1.2 #18

Merged
merged 6 commits into from
Oct 29, 2024
Merged
Show file tree
Hide file tree
Changes from 5 commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
76 changes: 38 additions & 38 deletions .github/PULL_REQUEST_TEMPLATE.md
Original file line number Diff line number Diff line change
@@ -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.
3 changes: 3 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
6 changes: 2 additions & 4 deletions Dockerfile
Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
FROM ubuntu:20.04
FROM ubuntu:23.04

Check notice on line 1 in Dockerfile

View check run for this annotation

Wiz Inc. (8da00b022c) / Wiz IaC Scanner

Healthcheck Instruction Missing

Rule ID: b0f1f03a-461a-4b7b-8daf-a61ca12d86da Severity: Low Resource: FROM={{ubuntu:23.04}} Ensure that HEALTHCHECK is being used. The HEALTHCHECK instruction tells Docker how to test a container to check that it is still working
Raw output
Expected: Dockerfile should contain instruction 'HEALTHCHECK'
Found: Dockerfile doesn't contain instruction 'HEALTHCHECK'

ARG MUSE_VERSION=2.0.4
ARG MUSE_SHA512=8342e648d389b7feef04f870c48bcddbbbdfc85e0c5faf261e6bf68e2f48a02be3e3251691004cf7bb0164de25dc1ef8323dbe5eabc040ba54740c034337a997
yashpatel6 marked this conversation as resolved.
Show resolved Hide resolved
ARG MUSE_VERSION=2.1.2
ARG DEBIAN_FRONTEND=noninteractive

RUN apt-get update && apt-get install -y --no-install-recommends \
Expand All @@ -12,7 +11,6 @@

WORKDIR /src/
RUN wget https://github.com/wwylab/MuSE/archive/refs/tags/v${MUSE_VERSION}.zip \
&& echo "${MUSE_SHA512} v${MUSE_VERSION}.zip" | sha512sum --strict -c \
&& unzip v${MUSE_VERSION}.zip && rm v${MUSE_VERSION}.zip

RUN cd /src/MuSE-${MUSE_VERSION} && bash ./install_muse.sh
Expand Down
4 changes: 2 additions & 2 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ MuSE documentation is [here](https://github.com/wwylab/MuSE).
# Version
| Tool | Version |
|------|---------|
|MuSE| 2.0.4|
|MuSE| 2.1.2|


---
Expand All @@ -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.

Expand Down
2 changes: 1 addition & 1 deletion metadata.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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'