yangwu91 / bioinfo-docker Goto Github PK

This is a Docker image with Bioinformatics utilities preinstalled, enjoy!

• Python=3.11
• R=4
• Built on the latest ubuntu:focal docker
• Used the BFSU mirror as default
• Pre-installed some useful applications (i.e. wget, vim, git etc.)
• Pre-installed some latest bioinformatics tools:
  • samtools
  • bowtie2
  • bedtools
  • bwa
  • hisat2
  • blast
  • fastqc
  • minimap2
• Pre-installed some R packages:
  • tidyverse
  • ggplot2
  • edgeR
  • DESeq2

# To pull the image:
docker pull yangwu91/bioinfo
# To use the Docker bash:
docker run -it yangwu91/bioinfo
# For quick one-time use:
docker run -it -v /dev/shm:/dev/shm -v /home/user/data:/workspace yangwu91/bioinfo blastn -query /workspace/query.fasta -db /workspace/db -out /workspace/out.blastn

Example workflow to set up Conda with Bioconda and other channels:

name: bioinfo
  
on:
  release:
    types: [published]
  
jobs:
  bioconda:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v3
    - name: Set up bioconda and other custom channels
      uses: yangwu91/[email protected]
      with:
          mirror: 'bfsu'
          channels: 'yangwu91'
          packages: 'r2g diamond'
          cmd: 'r2g --version; diamond --version'
          args: 'conda info'