From 2a9dc25964937309ce40603f0f8fd928c72aff6c Mon Sep 17 00:00:00 2001 From: Mohammed Faizal Eeman Mootor <68152431+Faizal-Eeman@users.noreply.github.com> Date: Mon, 24 Oct 2022 17:02:28 -0700 Subject: [PATCH] Update Delly 1.1.5 (#12) * closes #11 - update Delly to v1.1.5 * Update CHANGELOG.md * Update metadata.yaml * Update README.md * Add Docker-build-release.yaml * Update .gitignore * change Image_name to image_name in Docker-build-release.yaml * Update README.md * Update CHANGELOG.md * Update Docker-build-release.yaml * fix yaml linting in Docker-build-release.yaml Co-authored-by: Mootor --- .github/workflows/Docker-build-release.yaml | 20 ++++++ .gitignore | 75 ++++++++++++++++++++- CHANGELOG.md | 10 +++ Dockerfile | 2 +- README.md | 10 +-- metadata.yaml | 18 ++--- 6 files changed, 119 insertions(+), 16 deletions(-) create mode 100644 .github/workflows/Docker-build-release.yaml diff --git a/.github/workflows/Docker-build-release.yaml b/.github/workflows/Docker-build-release.yaml new file mode 100644 index 0000000..b2313d4 --- /dev/null +++ b/.github/workflows/Docker-build-release.yaml @@ -0,0 +1,20 @@ +--- +on: + push: + branches: ['main'] + tags: ['v*'] + release: + types: [published] + +jobs: + build-and-push-image: + runs-on: ubuntu-latest + name: A job to build and push a docker image + permissions: + contents: read + packages: write + steps: + - id: build-push + uses: uclahs-cds/tool-Docker-action/build-release@latest + with: + github-token: ${{ secrets.GITHUB_TOKEN }} diff --git a/.gitignore b/.gitignore index e0a1def..faa68e8 100644 --- a/.gitignore +++ b/.gitignore @@ -1,8 +1,81 @@ # System files +*.log .DS_Store # R .Rhistory .Rapp.history .Rproj.user -.RData +*.RData +*.rd[as] + +# Python +__pycache__/ +.pytest_cache/ +.Python +pip-log.txt +pip-delete-this-directory.txt +*.py[cod] +*$py.class +venv +.venv +.env + +# VScode +.vscode + +# Nextflow +work/ +.nextflow/ +*.nextflow.log* + +## Molecular files + +# Array file +*.CEL +*.cel +*.OSCHP + +# Sequence file (e.g. Reference genome) +*.fasta +*.fa +*.fai +*.dict +*.gtf + +# FASTQ file +*.fq +*.fastq + +# Proteomics file +*.raw +*.mzML +*.mzXML +*.mgf +*.idXML +*.consensusXML +*.featureXML +*.mzid +*.mzData +*.dta +*.dta2d + +# DNA/RNA alignment file +*.sam +*.bam +*.bai +*.cram +*.crai + +# Variant file +*.bcf +*.csi +*.vcf +*.tbi +*.maf + +# Compressed file +*.gz +*.tar +*.zip + diff --git a/CHANGELOG.md b/CHANGELOG.md index 2868585..ebea5f0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,16 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm --- +## [1.1.5] - 2022-10-24 +### Added +- Add `Docker-build-release.yaml` to the repo + +### Changed +- Update Delly v1.1.5 in Dockerfile +- Update `.gitignore` file + +--- + ## [1.1.3] - 2022-08-03 ### Changed - Replace `conda` with `mamba` in Dockerfile based on the BL Docker Template diff --git a/Dockerfile b/Dockerfile index 4a40850..23902ba 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,7 +1,7 @@ FROM blcdsdockerregistry/bl-base:1.1.0 AS builder # Use conda to install tools and dependencies into /usr/local -ARG DELLY_VERSION=1.1.3 +ARG DELLY_VERSION=1.1.5 RUN mamba create -qy -p /usr/local \ -c bioconda \ -c conda-forge \ diff --git a/README.md b/README.md index 54b0300..7b423a2 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ -# docker-delly +# docker-Delly Repository for the Boutros Lab Delly Dockerfile, "an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data." -The image is located in the Boutros Lab Docker Hub repo: https://hub.docker.com/repository/docker/blcdsdockerregistry/delly +This image can be found in docker-Delly's GitHub package page [here](https://github.com/uclahs-cds/docker-Delly/pkgs/container/delly). # Documentation Delly GitHub repository [here](https://github.com/dellytools/delly) @@ -10,7 +10,7 @@ Delly GitHub repository [here](https://github.com/dellytools/delly) # Version | Tool | Version | |------|---------| -|Delly| 1.1.3| +|Delly| 1.1.5| --- @@ -28,9 +28,9 @@ https://doi.org/10.1093/bioinformatics/bts378 Author: 'Timothy Sanders', 'Yu Pan', 'Mohammed Faizal Eeman Mootor' -docker-delly is licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license. +docker-Delly is licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license. -docker-delly can be used to create a docker instance to use the Delly tool. +docker-Delly can be used to create a docker instance to use the Delly tool. Copyright (C) 2021-2022 University of California Los Angeles ("Boutros Lab") All rights reserved. diff --git a/metadata.yaml b/metadata.yaml index f7e3949..9da58dc 100644 --- a/metadata.yaml +++ b/metadata.yaml @@ -1,10 +1,10 @@ --- -Category: 'docker' -Description: 'Docker repository for Delly' -Maintainers: ['yupan@mednet.ucla.edu', 'mmootor@mednet.ucla.edu'] -Contributors: ['Timothy Sanders', 'Yu Pan', 'Mohammed Faizal Eeman Mootor'] -Languages: ['Dockerfile'] -Tools: ['Delly'] -Version: ['1.1.3'] -Purpose of tool: 'Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data.' -References: 'https://github.com/dellytools/delly' +category: 'docker' +description: 'Docker repository for Delly' +maintainers: ['yupan@mednet.ucla.edu', 'mmootor@mednet.ucla.edu'] +languages: ['Dockerfile'] +tools: ['Delly'] +version: ['1.1.5'] +purpose: 'Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data.' +references: 'https://github.com/dellytools/delly' +image_name: 'delly'