Bioconda with Docker and GitHub Actions

This is the Bioconda integrated with Docker and GitHub Actions, enjoy! N.B., this is NOT the official repository.

Environments

• Python=3.8
• 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=1.10
  • bowtie2=2.4.1
  • bedtools=2.29.2
  • bwa=0.7.17
  • hisat2=2.2.1
  • blast=2.10.1
  • fastqc=0.11.9
  • minimap2=2.17
• Pre-installed some R packages:
  • ggplot2=3.3.2
  • edgeR=3.30.0
  • DESeq2=1.28.0

Docker image

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

GitHub Actions

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

name: bioconda
  
on:
  release:
    types: [published]
  
jobs:
  bioconda:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v2
    - name: Set up bioconda and other custom channels
      uses: yangwu91/bioconda@1.0
      with:
          mirror: 'bfsu'
          channels: 'yangwu91'
          packages: 'r2g diamond'
          cmd: 'r2g --version; diamond --version'
          args: 'conda info'