yangwu91/bioinfo
Integrated with bioinformatics utilities
Image
0
479
yangwu91/bioinfo repository overview
Bioconda with Docker and GitHub Actions
This is a Docker image with Bioinformatics utilities preinstalled, enjoy!
Environments
- Python=3.10
- 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
Docker image
# 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
GitHub Actions
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'
Tag summary
Content type
Image
Digest
sha256:af269dba3…
Size
2.1 GB
Last updated
over 2 years ago
docker pull yangwu91/bioinfo