rnakato/database repository overview

⁠docker_database

Docker image to download reference data and make index files. This is the base image for Churros⁠ and RumBall⁠.

• 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

• SAMtools 1.19.2

• SRAtoolkit 3.0.10

• BEDtools 2.31.0

• OpenBLAS 0.3.24

• user:password

  • ubuntu:ubuntu

• DockerHub:

  • https://hub.docker.com/r/rnakato/database⁠
  • https://hub.docker.com/r/rnakato/database_gpu⁠

⁠Changelog

• 2024.02

  • Installed sudo
  • Updated Miniconda from Python 3.9 to Python 3.10

• 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)

• 2023.11

  • Removed LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/compat/:/usr/local/cuda/lib64

• 2023.10

  • Added LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/compat/:/usr/local/cuda/lib64

• 2023.06

  • Added fish

• 2022.09

  • Added UCSC build as a argument
  • Update bedtools from v2.30.0 to v2.31.0

• Ensembl106

• This image is based on Ensembl version 106

⁠Usage

Run normal image:

docker run -it --rm rnakato/database /bin/bash

Run with GPU:

docker run -it --rm --gpus all rnakato/database_gpu /bin/bash

The default user is ubuntu. Add -u root if you want to login as root:

docker run -it --rm --gpus all -u root rnakato/database_gpu /bin/bash

⁠Build images from Dockerfile

# normal
docker build -t youracount/database --target normal .
# with GPU
docker build -t youracount/database_gpu --target gpu .