Merge pull request #1 from uclahs-cds/initial-branch

Dockerfile for Samtools

.github/ISSUE_TEMPLATE/issue_report.md

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+---
+name: Docker Issue report
+about: Create a report to help us improve our Docker images
+title: "[DOCKER_ISSUE]"
+labels: ''
+assignees: ''
+
+---
+
+**Describe the issue**
+A clear and concise description of what the issue is. Please include the following in your issue report along with any explicit errors observed
+* Docker image release version
+* Cluster you are using (SGE/Slurm-Dev/Slurm-Test)
+* Config files (if applicable)
+* Path to the working directory
+* Any logs produced by the pipeline
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Additional context**
+Add any other context about the problem here.

CHANGELOG.md

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+# Changelog
+All notable changes to the Samtools Dockerfile.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
+
+This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+---
+
+## [1.0.0] - 2021-04-28
+### Added
+- git repo created
+- Samtools 1.11

Dockerfile

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+FROM blcdsdockerregistry/bl-base:1.0.0 AS builder
+
+# Use conda to install tools and dependencies into /usr/local
+ARG SAMTOOLS_VERSION=1.11
+RUN conda create -qy -p /usr/local \
+    -c bioconda \
+    -c conda-forge \
+    samtools==${SAMTOOLS_VERSION}
+
+# Deploy the target tools into a base image
+FROM ubuntu:20.04
+COPY --from=builder /usr/local /usr/local
+
+LABEL maintainer="Rupert Hugh-White <[email protected]>"

README.md

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+# docker-samtools
+Dockerfile for samtools - a tools for "Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format".
+
+Boutros Lab Docker Hub repo: https://hub.docker.com/r/blcdsdockerregistry/samtools
+
+# Documentation
+Samtools documentation [here](http://www.htslib.org/doc/samtools.html).
+
+# Version
+| Tool | Version |
+|------|---------|
+|Samtools| 1.11|
+
+
+---
+
+## References
+
+1. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, and 1000 Genome Project Data Processing Subgroup, The Sequence alignment/map (SAM) format and SAMtools, Bioinformatics (2009) 25(16) 2078-9.
+2. Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H, Twelve years of SAMtools and BCFtools, GigaScience (2021) 10(2).

metadata.yaml

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 ---
-Category: '' # shoule be one of docker/pipeline/project/template/tool/training/users
-Description: '' # Description of why the repository exists
-Maintainers: ['[email protected]', '[email protected]'] # email address of maintainers
-Contributors: 'Xavier Hernandez' # Full names of contributors
-Languages: ['R', 'perl', 'nextflow'] # programming languages used
-Dependencies: 'BPG' # packages, tools that repo needs to run
-References: '' # is the tool/dependencies published, is there a confluence page
+Category: 'docker'
+Description: 'Docker repository for Samtools'
+Maintainers: ['[email protected]']
+Contributors: ['Rupert Hugh-White']
+Languages: ['Docker', 'bash']
+Tools: ['Samtools']
+Version: ['1.11']
+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)'