Singularity containers for bioinformatics tools

Bioinformatics related singularity container recipies.

Base is CentOS 8.

Currently two containers are implemented:

• basic tools:
  • Samtools
  • BEDTools
  • FastQC
  • Bowtie2
  • MultiQC
  • Cutadapt
  • STAR
  • Hisat2
  • Picard
  • Trimmomatic
  • Samblaster
  • VarScan
  • Vcfanno
  • Plink
  • MACS2
  • Homer
  • NextFlow
  • nf-core
  • MAGeCK
  • TrimGalore
  • Bismark
  • UCSC tools
• methylKit (built from basic):
  • R + Bioconductor
  • methylkit
• samtools (built from Alpine Linux 3.10.3)
  • Note, automated Singularity Hub build does not seem to work correctly as this recipe uses multistage build to minimize container size

Availability

Basic tools container is available at Singularity hub: shub://thakk/biobase