Merge pull request #1 from uclahs-cds/maotian-create-initial-commit

Create docker image for bam-readcount 0.8.0

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,56 @@
+## Description
+
+<!--Provide a brief summary of the PR here-->
+
+<!--- 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 updated the version number/dependencies and added my name to the maintainer listing 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 listing 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 addidtions/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 A-mini 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```
+
+<!--- 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
+
+Closes #<!--Issue #-->
+
+- 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

@@ -8,30 +8,9 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ---
 
 ## [Unreleased]
-### Changed
-- Changed something but it is not part of the last release.
 
 ---
 
-## [1.0.0] - YYYY-MM-DD
+## [0.8.0] - 2021-11-02
 ### Added
-- For new features.
-- Added item 1.
-
-### Changed
-- For changes in existing functionality.
-- Changed item 1.
-
-### Deprecated
-- For soon-to-be removed features.
-
-### Removed
-- For now removed features.
-- Removed item 1.
-
-### Fixed
-- For any bug fixes.
-- Fixed item 1.
-
-### Security
-- In case of vulnerabilities.
+- Create dockerfile for bam-readcount 0.8.0.

Dockerfile

@@ -1,14 +1,30 @@
-FROM blcdsdockerregistry/bl-base:1.0.0 AS builder
+FROM ubuntu:20.04
+ARG BAM_READCOUNT_VERSION=0.8.0
+ARG BAM_READCOUNT_SHA512=ef2acdc9e9b581cb0e4ccea51e3cb445394733f9812f68790a171b71d5f2f089f73aa39a62a6ddf372baa174b884f7d1e52f3f2c9a2abb716599fd7832501a97
+RUN apt-get update \
+    && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends\
+    build-essential \
+    git-core \
+    cmake \
+    zlib1g-dev \
+    libncurses-dev \
+    patch \
+    wget \
+    ca-certificates \
+    && rm -rf /var/lib/apt/lists/*
 
-# Use conda to install tools and dependencies into /usr/local
-ARG TOOL_VERSION=X.X.X
-RUN conda create -qy -p /usr/local \
-    -c bioconda \
-    -c conda-forge \
-    tool_name==${TOOL_VERSION}
+WORKDIR /
+RUN wget https://github.com/genome/bam-readcount/archive/refs/tags/v${BAM_READCOUNT_VERSION}.tar.gz && \
+    echo "${BAM_READCOUNT_SHA512} v${BAM_READCOUNT_VERSION}.tar.gz" | sha512sum --strict -c - && \
+    tar xzf v${BAM_READCOUNT_VERSION}.tar.gz &&\
+    rm v${BAM_READCOUNT_VERSION}.tar.gz
 
-# Deploy the target tools into a base image
-FROM ubuntu:20.04
-COPY --from=builder /usr/local /usr/local
+RUN mkdir bam-readcount \
+    && cd bam-readcount \
+    && cmake /bam-readcount-${BAM_READCOUNT_VERSION} \
+    && make \
+    && rm -rf /bam-readcount-v${BAM_READCOUNT_VERSION} \
+    && ln -s /bam-readcount/bin/bam-readcount /usr/local/bin/bam-readcount
 
-LABEL maintainer="Your Name <[email protected]>"
+WORKDIR /app
+CMD ["bash"]

README.md

@@ -1,38 +1,39 @@
-# docker-tool_name
-Template Repository for the Boutros Lab Dockerfiles based on the bl-base image.
+# docker-bam-readcount
+Bam-readcount is a utility that counts DNA sequence reads in BAM and CRAM files. It generates metrics for `.bam` files at single nucleotide positions:
+```
+Usage: bam-readcount [OPTIONS] <bam_file> [region]
+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 bl-base image is located in the Boutros Lab Docker Hub repo: https://hub.docker.com/repository/docker/blcdsdockerregistry/bl-base
+The bam-readcount image is located in the Boutros Lab Docker Hub repo [here](https://hub.docker.com/repository/docker/blcdsdockerregistry/bam-readcount).
 
 # Documentation
-Docker introduction [here](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Docker+Introduction)
+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).
 
-Dockerfile Best Practices [here](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Dockerfile+Best+Practices)
-
-Docker image versioning standard [here](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Docker+image+versioning+standardization)
+The Boutros lab docker image versioning standard [here](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Docker+image+versioning+standardization).
 
 
 # Version
 | Tool | Version |
 |------|---------|
-|tool_name| X.X.X|
-|tool_name_2|X.X.X|
-
+|bam-readcount| 0.8.0|
 
 ---
 
 ## References
 
-1. Tool specific references can be listed here
+1. Khanna, Ajay et al. “Bam-readcount -- rapid generation of basepair-resolution sequence metrics.” ArXiv arXiv:2107.12817v1. 27 Jul. 2021 Preprint. 
 
 ---
 
 ## License
 
-Author: Name1, Name2
+Author: Caden Bugh, Mao Tian
 
-[docker repo name] 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 licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license.
 
-<one line to give the program's name and a brief idea of what it does.>
+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.
 

metadata.yaml

@@ -1,10 +1,10 @@
 ---
 Category: 'docker'
-Description: 'Template Docker repository for tool_name'  # Description of why the repository exists
-Maintainers: ['YourName@mednet.ucla.edu']  # email address of maintainers
-Contributors: ['Your Name']  # Full names of contributors
+Description: 'Docker repository for bam-readcount'  # Description of why the repository exists
+Maintainers: ['[email protected]', 'maotian@mednet.ucla.edu']  # email address of maintainers
+Contributors: ['Caden Bugh', 'Mao Tian']  # Full names of contributors
 Languages: ['Dockerfile']  # programming languages used
-Tools: ['tool_name']  # Name of the tool(s) used in the Dockerfile
-Version: ['X.X.X']  # Tool version number
-Purpose of tool: ''  # Description of what this tool does
-References: ''  # is the tool/dependencies published, is there a confluence page
+Tools: ['bam-readcount']  # Name of the tool(s) used in the Dockerfile
+Version: ['0.8.0']  # 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