Merge pull request #3 from uclahs-cds/abesh-update-samtools-1.14

Update to SAMtools v1.14

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,61 @@
+<!--- Please read each of the following items and confirm by replacing the [ ] with a [X] --->
+## Checklist 
+
+### Formatting
+
+- [ ] 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).
+
+- [ ] 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].
+
+- [ ] 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.
+
+### File Updates
+
+- [ ] I have ensured that the version number update follows the [versioning standards](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Docker+image+versioning+standardization).
+
+- [ ] I have updated the version number/dependencies and added my name to the maintainer list in the `Dockerfile`.
+
+- [ ] I have updated the version number/feature changes in the `README.md`.
+
+<!--- 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`.
+
+- [ ] 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.
+
+<!---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. 
+
+### Docker Hub Auto Build Rules
+
+- [ ] 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).
+
+### Docker Image Testing
+
+- [ ] I have tested the Docker image with the `docker run` command as described below.
+
+#### Test the Docker image with at least one sample. Verify the new Docker image works using:
+
+```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>```
+
+#### My command: 
+
+```Provide the command you ran here```
+
+## Description
+
+<!--- Briefly describe the changes included in this pull request
+ !--- starting with 'Closes #...' if approriate --->
+
+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
+
+- 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-->

CHANGELOG.md

@@ -8,6 +8,13 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ---
 ## [Unreleased]
 
+## [1.14] 2022-02-14
+### Updated
+- Update to SAMtools 1.14
+- Install SAMtools using mamba
+### Added
+- Add bldocker user/group to container
+
 ## [1.12] - 2021-05-24
 ### Added
 - Update to SAMtools 1.12

Dockerfile

@@ -1,8 +1,8 @@
-FROM blcdsdockerregistry/bl-base:1.0.0 AS builder
+FROM blcdsdockerregistry/bl-base:1.1.0 AS builder
 
-# Use conda to install tools and dependencies into /usr/local
-ARG SAMTOOLS_VERSION=1.12
-RUN conda create -qy -p /usr/local \
+# Use mamba to install tools and dependencies into /usr/local
+ARG SAMTOOLS_VERSION=1.14
+RUN mamba create -qy -p /usr/local \
     -c bioconda \
     -c conda-forge \
     samtools==${SAMTOOLS_VERSION}
@@ -11,4 +11,11 @@ RUN conda create -qy -p /usr/local \
 FROM ubuntu:20.04
 COPY --from=builder /usr/local /usr/local
 
+# Add a new user/group called bldocker
+RUN groupadd -g 500001 bldocker && \
+    useradd -r -u 500001 -g bldocker bldocker
+
+# Change the default user to bldocker from root
+USER bldocker
+
 LABEL maintainer="Rupert Hugh-White <[email protected]>"

README.md

@@ -9,7 +9,7 @@ SAMtools documentation [here](http://www.htslib.org/doc/samtools.html).
 # Version
 | Tool | Version |
 |------|---------|
-|SAMtools| 1.12|
+|SAMtools| 1.14|
 
 
 ---

metadata.yaml

@@ -2,10 +2,9 @@
 Category: 'docker'
 Description: 'Docker repository for SAMtools'
 Maintainers: ['[email protected]']
-Contributors: ['Rupert Hugh-White', 'Helena Winata']
-Languages: ['Docker', 'bash']
+Contributors: ['Rupert Hugh-White', 'Helena Winata', 'Arpi Beshlikyan']
+Languages: ['Dockerfile']
 Tools: ['SAMtools']
-Version: ['1.12']
+Version: ['1.14']
 Purpose: 'A tool for reading/writing/editing/indexing/viewing SAM/BAM/CRAM format'
-Dependencies: ['docker', 'conda', 'bl-base']
 References: 'Li H et al. Bioinformatics 25, (2009)'