scanpy_seurat.def

Bootstrap: docker

From: satijalab/seurat:latest #4.3.0

%setup

%post

  # install system dpt 
  apt-get update
  apt install -y libfontconfig1-dev libharfbuzz-dev libfribidi-dev
  apt install -y libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev libgit2-dev

  # downgrade numpy because scanpy is broken then
  pip3 install numpy==1.23.1 

  # install notebook and plotting basics
  pip3 install jupyterlab
  pip3 install ipywidgets
  pip3 install pandas
  pip3 install seaborn
  
  # install scanpy
  pip3 install scanpy
  pip3 install leidenalg

  # bio python
  pip3 install scikit-bio

  # sklearn
  pip3 install scikit-learn

  # R dpt
  # Install missing packages for tutorial
  R --no-echo --no-restore --no-save -e "install.packages(c('devtools'))"
  R --no-echo --no-restore --no-save -e "devtools::install_github('satijalab/seurat-data')"
  R --no-echo --no-restore --no-save -e "install.packages('metap')"
  R --no-echo --no-restore --no-save -e "install.packages(c('data.table','lattice'))"
  R --no-echo --no-restore --no-save -e "install.packages('IRkernel')"
  R --no-echo --no-restore --no-save -e "IRkernel::installspec(user=F, sys_prefix=T)"
  R --no-echo --no-restore --no-save -e "devtools::install_github('satijalab/seurat-data')"
  R --no-echo --no-restore --no-save -e "SeuratData::InstallData(ds = c('pbmc3k','thp1.eccite'))"
  R --no-echo --no-restore --no-save -e "devtools::install_github('satijalab/sctransform', ref='develop')"
  # Install packages for BD scripts
  R --no-echo --no-restore --no-save -e "install.packages(c('tidyverse'))"
  R --no-echo --no-restore --no-save -e "devtools::install_github('vibscc/DALI')"
  R --no-echo --no-restore --no-save -e "devtools::install_github('dynverse/dyno')"

%runscript
  R