From 055f232e0bb6058beeb20a5d28cca78d0ca792ab Mon Sep 17 00:00:00 2001 From: Rupert Hugh-White <61213624+rhughwhite@users.noreply.github.com> Date: Mon, 26 Apr 2021 11:43:42 -0700 Subject: [PATCH 1/9] Create Dockerfile --- Dockerfile | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 Dockerfile diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..1959c45 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,14 @@ +FROM blcdsdockerregistry/bl-base:1.0.0 AS builder + +# Use conda to install tools and dependencies into /usr/local +ENV 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 " From 815a98c070d55d008b2a9cbc48cacb7f7f8bce8a Mon Sep 17 00:00:00 2001 From: Rupert Hugh-White <61213624+rhughwhite@users.noreply.github.com> Date: Mon, 26 Apr 2021 11:47:31 -0700 Subject: [PATCH 2/9] Update metadata.yaml --- metadata.yaml | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/metadata.yaml b/metadata.yaml index cbe8aa9..d0169cd 100644 --- a/metadata.yaml +++ b/metadata.yaml @@ -1,8 +1,11 @@ --- -Category: '' # shoule be one of docker/pipeline/project/template/tool/training/users -Description: '' # Description of why the repository exists -Maintainers: ['someone@mednet.ucla.edu', 'someoneelse@mednet.ucla.edu'] # 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: 'Dockerfile for Samtools' +Maintainers: ['rhughwhite@mednet.ucla.edu'] # email address of maintainers +Contributors: 'Rupert Hugh-White' # Full names of contributors +Languages: ['Docker', 'shell script'] # programming languages used +Tools: ['Samtools'] +Version: ['1.11'] +Purpose: 'A tool for reading/writing/editing/indexing/viewing SAM/BAM/CRAM format' +Dependencies: ['docker'] # packages, tools that repo needs to run +References: 'Li H et al. Bioinformatics 25, (2009)' From 86001c9e2d6b20ba67e84478ebdba5a82f663eef Mon Sep 17 00:00:00 2001 From: Rupert Hugh-White <61213624+rhughwhite@users.noreply.github.com> Date: Mon, 26 Apr 2021 11:50:24 -0700 Subject: [PATCH 3/9] Create README.md --- README.md | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 README.md diff --git a/README.md b/README.md new file mode 100644 index 0000000..5497e0d --- /dev/null +++ b/README.md @@ -0,0 +1,17 @@ +# docker-samtools +Dockerfile for samtools - a tools for "Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format". + +The image is located in the BLCDS repo: https://hub.docker.com/r/blcdsdockerregistry/samtools + +# Documentation +Samtools documentation [here](http://www.htslib.org/doc/samtools.html). + +# Version +Current version: 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). From 1308345286d790f10a0d25cfad5cd3e8433b462c Mon Sep 17 00:00:00 2001 From: Rupert Hugh-White <61213624+rhughwhite@users.noreply.github.com> Date: Wed, 28 Apr 2021 10:29:20 -0700 Subject: [PATCH 4/9] Create issue_report.md --- .github/ISSUE_TEMPLATE/issue_report.md | 32 ++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 .github/ISSUE_TEMPLATE/issue_report.md diff --git a/.github/ISSUE_TEMPLATE/issue_report.md b/.github/ISSUE_TEMPLATE/issue_report.md new file mode 100644 index 0000000..1cab286 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/issue_report.md @@ -0,0 +1,32 @@ +--- +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. From af351ae363e49ebd8b7630488ba1b393155bb115 Mon Sep 17 00:00:00 2001 From: Rupert Hugh-White <61213624+rhughwhite@users.noreply.github.com> Date: Wed, 28 Apr 2021 10:49:53 -0700 Subject: [PATCH 5/9] Create CHANGELOG.md --- CHANGELOG.md | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 CHANGELOG.md diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..9c89213 --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,13 @@ +# 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 From f1810c4f02766b0ea289adacfaa8d60cb9895688 Mon Sep 17 00:00:00 2001 From: Rupert Hugh-White <61213624+rhughwhite@users.noreply.github.com> Date: Wed, 28 Apr 2021 11:19:42 -0700 Subject: [PATCH 6/9] Change format to match docker-template --- metadata.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/metadata.yaml b/metadata.yaml index d0169cd..35a98ec 100644 --- a/metadata.yaml +++ b/metadata.yaml @@ -1,11 +1,11 @@ --- Category: 'docker' -Description: 'Dockerfile for Samtools' -Maintainers: ['rhughwhite@mednet.ucla.edu'] # email address of maintainers -Contributors: 'Rupert Hugh-White' # Full names of contributors -Languages: ['Docker', 'shell script'] # programming languages used +Description: 'Template Docker repository for Samtools' +Maintainers: ['rhughwhite@mednet.ucla.edu'] +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'] # packages, tools that repo needs to run +Dependencies: ['docker', 'conda', 'bl-base'] References: 'Li H et al. Bioinformatics 25, (2009)' From 1bdcd83ed6c9861a4de79e8c14a81424aa607a03 Mon Sep 17 00:00:00 2001 From: Rupert Hugh-White <61213624+rhughwhite@users.noreply.github.com> Date: Wed, 28 Apr 2021 11:26:02 -0700 Subject: [PATCH 7/9] Add version table --- README.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 5497e0d..0488d8b 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,16 @@ # docker-samtools Dockerfile for samtools - a tools for "Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format". -The image is located in the BLCDS repo: https://hub.docker.com/r/blcdsdockerregistry/samtools +Boutros Lab Docker Hub repo: https://hub.docker.com/r/blcdsdockerregistry/samtools # Documentation Samtools documentation [here](http://www.htslib.org/doc/samtools.html). # Version -Current version: 1.11 +| Tool | Version | +|------|---------| +|Samtools| 1.11| + --- From 5936ef57d06ea3649f993260efd21308cab949ea Mon Sep 17 00:00:00 2001 From: Rupert Hugh-White <61213624+rhughwhite@users.noreply.github.com> Date: Wed, 28 Apr 2021 11:35:56 -0700 Subject: [PATCH 8/9] Change ENV to ARG --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 1959c45..816a18c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,7 +1,7 @@ FROM blcdsdockerregistry/bl-base:1.0.0 AS builder # Use conda to install tools and dependencies into /usr/local -ENV SAMTOOLS_VERSION=1.11 +ARG SAMTOOLS_VERSION=1.11 RUN conda create -qy -p /usr/local \ -c bioconda \ -c conda-forge \ From 03e7e21ad35deb4d6fed34a3106c859f25d404ae Mon Sep 17 00:00:00 2001 From: Rupert Hugh-White <61213624+rhughwhite@users.noreply.github.com> Date: Wed, 28 Apr 2021 17:43:31 -0700 Subject: [PATCH 9/9] remove 'Template' from description --- metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metadata.yaml b/metadata.yaml index 35a98ec..0a234b2 100644 --- a/metadata.yaml +++ b/metadata.yaml @@ -1,6 +1,6 @@ --- Category: 'docker' -Description: 'Template Docker repository for Samtools' +Description: 'Docker repository for Samtools' Maintainers: ['rhughwhite@mednet.ucla.edu'] Contributors: ['Rupert Hugh-White'] Languages: ['Docker', 'bash']