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Faizal-EemanMootor
Faizal-Eeman
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Mootor
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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 <mmootor@ip-0A12521C.rhxrlfvjyzbupc03cc22jkch3c.xx.internal.cloudapp.net>
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‎.github/workflows/Docker-build-release.yaml

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---
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on:
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push:
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branches: ['main']
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tags: ['v*']
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release:
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types: [published]
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jobs:
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build-and-push-image:
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runs-on: ubuntu-latest
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name: A job to build and push a docker image
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permissions:
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contents: read
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packages: write
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steps:
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- id: build-push
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uses: uclahs-cds/tool-Docker-action/build-release@latest
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with:
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github-token: ${{ secrets.GITHUB_TOKEN }}

‎.gitignore

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# System files
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*.log
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.DS_Store
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# R
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.Rhistory
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.Rapp.history
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.Rproj.user
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.RData
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*.RData
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*.rd[as]
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# Python
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__pycache__/
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.pytest_cache/
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.Python
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pip-log.txt
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pip-delete-this-directory.txt
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*.py[cod]
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*$py.class
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venv
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.venv
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.env
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# VScode
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.vscode
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# Nextflow
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work/
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.nextflow/
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*.nextflow.log*
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## Molecular files
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# Array file
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*.CEL
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*.cel
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*.OSCHP
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# Sequence file (e.g. Reference genome)
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*.fasta
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*.fa
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*.fai
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*.dict
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*.gtf
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# FASTQ file
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*.fq
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*.fastq
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# Proteomics file
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*.raw
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*.mzML
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*.mzXML
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*.mgf
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*.idXML
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*.consensusXML
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*.featureXML
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*.mzid
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*.mzData
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*.dta
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*.dta2d
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# DNA/RNA alignment file
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*.sam
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*.bam
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*.bai
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*.cram
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*.crai
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# Variant file
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*.bcf
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*.csi
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*.vcf
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*.tbi
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*.maf
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# Compressed file
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*.gz
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*.tar
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*.zip
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‎CHANGELOG.md

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---
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## [1.1.5] - 2022-10-24
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### Added
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- Add `Docker-build-release.yaml` to the repo
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### Changed
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- Update Delly v1.1.5 in Dockerfile
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- Update `.gitignore` file
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---
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## [1.1.3] - 2022-08-03
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### Changed
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- Replace `conda` with `mamba` in Dockerfile based on the BL Docker Template

‎Dockerfile

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FROM blcdsdockerregistry/bl-base:1.1.0 AS builder
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# Use conda to install tools and dependencies into /usr/local
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ARG DELLY_VERSION=1.1.3
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ARG DELLY_VERSION=1.1.5
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RUN mamba create -qy -p /usr/local \
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-c bioconda \
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-c conda-forge \

‎README.md

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# docker-delly
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# docker-Delly
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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."
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The image is located in the Boutros Lab Docker Hub repo: https://hub.docker.com/repository/docker/blcdsdockerregistry/delly
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This image can be found in docker-Delly's GitHub package page [here](https://github.com/uclahs-cds/docker-Delly/pkgs/container/delly).
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# Documentation
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Delly GitHub repository [here](https://github.com/dellytools/delly)
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# Version
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| Tool | Version |
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|------|---------|
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|Delly| 1.1.3|
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|Delly| 1.1.5|
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---
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Author: 'Timothy Sanders', 'Yu Pan', 'Mohammed Faizal Eeman Mootor'
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docker-delly is licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license.
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docker-Delly is licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license.
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docker-delly can be used to create a docker instance to use the Delly tool.
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docker-Delly can be used to create a docker instance to use the Delly tool.
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Copyright (C) 2021-2022 University of California Los Angeles ("Boutros Lab") All rights reserved.
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‎metadata.yaml

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---
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Category: 'docker'
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Description: 'Docker repository for Delly'
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Maintainers: ['[email protected]', '[email protected]']
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Contributors: ['Timothy Sanders', 'Yu Pan', 'Mohammed Faizal Eeman Mootor']
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Languages: ['Dockerfile']
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Tools: ['Delly']
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Version: ['1.1.3']
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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.'
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References: 'https://github.com/dellytools/delly'
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category: 'docker'
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description: 'Docker repository for Delly'
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maintainers: ['[email protected]', '[email protected]']
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languages: ['Dockerfile']
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tools: ['Delly']
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version: ['1.1.5']
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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.'
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references: 'https://github.com/dellytools/delly'
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image_name: 'delly'

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