amkorb / shortcake

A docker image for singlecell analysis

ShortCake🍰

A docker image for single-cell analyses. It's on docker-hub and GitHub. This repository is an update of singlecell_jupyter.

Changelog

• 2022.11.16

  • Rename to ShortCake 🍰

• 2022.08.2 (2022-08)

  • Create separate environments for python tools to avoid version conflict. They can be executed from Jupyter notebook

• 2022.03 (2022-03-03)

  • Separate Dockerfile to Dockerfile.R and Dockerfile.Python
  • change base image from pytorch-1.5-cuda10.1-cudnn7-devel to nvidia/cuda:11.5.1-cudnn8-devel-ubuntu20.04 to upgrade Python to 3.9
  • Add CellChat, dyngen, Dynamo

• 2021.03 (2021-05-01):

  • Add datasets in SeuratData
  • Add Pagoda2

• 2021.02 (2021-02-07):

  • Add programs
  • Use pip venv for several tools to avoid package conflicts (e.g., tensorflow)

• 2020.12 (2020-12-24):

  • Add docker-compose.yml to allow GitHub Token
  • Omit the password to login Jupyter notebook
  • Add programs
  • Fix several bugs in the installation

• v1.3.0 (2020-07-14): add programs

• v1.2.0: change base image from Ubuntu18.04 to pytorch-1.5-cuda10.1-cudnn7-devel to allow GPU computing

• v1.1.0: change base image jupyter/datascience-notebook to Ubuntu18.04

Included tools (latest)

• Pipeline: Seurat (and wrappers), scater, scran, scanpy, scVI, monet, Pagoda2, kallisto (bustools)

• Doublet finding: Scrublet, DoubletFinder

• Batch correction and data integration: Harmony, scmap, scBio, SingleCellNet

• Clustering: SC3, metacell, SCCAF, Constclust, bigSCale2

• Cluster annotation: RCA, CellAssign, garnett, scCatch, SingleR

• Trajectory analysis: Monocle2/3, slingshot, Palantir, FROWMAP

• RNA velocity: velocyto, scVelo, CellRank, Dynamo

• Gene network: WGCNA, SCENIC (pySCENIC)

• Cell-to-cell interaction: CellPhoneDB, SingleCellSingnalR, scTensor, cell2cell, CellChat

• Data imputation: scImpute, MAGIC, SAVER, SAVER-X, SCRABBLE

• Multi-modal: LIGER, scAI, MOFA2

• Bulk deconvolution: SCDC, MuSiC

• Simulation: Splatter, dyngen

• Others: scGen, sleepwalk, singleCellHaystack, ComplexHeatmap

• scATAC-seq: cicero, chromVAR, ArchR, Signac, cisTopic, episcanpy

• Database (genome): BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Dmelanogaster.UCSC.dm6

• Database (gene): EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79

• Database (motif): JASPAR2016, JASPAR2018, JASPAR2020

• SeuratData: ifnb_3.1.0, panc8_3.0.2, pbmcsca_3.0.0, pbmc3k_3.1.4, celegans.embryo_0.1.0, cbmc_3.1.4, hcabm40k_3.0.0, thp1.eccite_3.1.5, stxBrain_0.1.1, stxKidney_0.1.0, bmcite_0.3.0, pbmcMultiome_0.1.2, ssHippo_3.1.4

Run

For Docker:

# pull docker image
docker pull rnakato/shortcake

# container login
docker run [--gpus all] --rm -it rnakato/shortcake /bin/bash
# jupyter notebook (see 'mnt/' directory in the notebook )
docker run [--gpus all] --rm -p 8888:8888 -v (your directory):/work/mnt rnakato/shortcake jupyternotebook.sh

For Singularity:

# build image
singularity build -F shortcake.sif docker://rnakato/shortcake
# jupyter notebook
singularity exec [--nv] shortcake.sif jupyternotebook.sh
# execute R directory
singularity exec [--nv] shortcake.sif R

Build image from Dockerfile

First clone and move to the repository

git clone https://github.com/rnakato/ShortCake
cd ShortCake

• Because the Dockerfile installs many packages from GitHub, first get a GitHub token from your own repository and add it in Docker_R/docker-compose.R.yml and Docker_Python/docker-compose.yml.
• Download the dataset of SeuratData from our GoogleDrive and unzip it in Docker_R directory.

Then build packages:

# build R packages
cd Docker_R
docker-compose -f docker-compose.R.yml build
# Then build Python packages
cd ../Docker_Python/
docker-compose -f docker-compose.yml build

Contact

Ryuichiro Nakato: rnakato AT iqb.u-tokyo.ac.jp