rnakato/mapping repository overview

⁠docker_mapping

Repository of Docker image for mapping tools (based on Ubuntu 22.04)

• Ubuntu 22.04

• GPU mode (cuda:11.8.0-cudnn8-runtime)

  • CUDA 11.8
  • cudnn 8

• Perl 5.36.0 (with plenv)

• Python 3.10 (with Miniconda)

  • MACS2-2.2.9.1

• R 4.x

  • BiocManager
  • Rstudio Desktop
  • Rstudio Server

• BWA v0.7.17

• Bowtie v1.3.1

• Bowtie2 v2.5.3

• chromap v0.2.5

• SAMtools v1.19.2

• BEDtools v2.31.0

• SRAtoolkit v3.0.10

• OpenBLAS v0.3.24

⁠Changelog

• 2024.02

  • Installed sudo
  • Updated Miniconda from Python 3.9 to Python 3.10
  • Updated Bowtie2 from v2.4.5 to v2.5.3
  • Updated chromap from v0.2.4 to v0.2.5

• 2024.01

  • Updated SAMtools from 1.17 to 1.19.2
  • Updated SRAtoolkit from 3.0.2 to 3.0.10
  • Change WORKDIR from /opt to /home/ubuntu

• 2023.12

  • Update ChIPseqTools (ssp v1.3.1 and drompa+ v1.18.1)

⁠Usage

For Docker:

# pull docker image
docker pull rnakato/mapping

# execute bwa
docker run --rm -it rnakato/mapping bwa

For Singularity:

# build image
singularity build -F rnakato_mapping.sif docker://rnakato/mapping
# execute bwa
singularity exec rnakato_mapping.sif bwa

⁠Build image from Dockerfile

git clone https://github.com/rnakato/docker_mapping.git
cd docker_mapping
docker build -t <account>/mapping .