dcgc-bfx/dcgc-jupyter-rstudio:latest
$ singularity pull shub://dcgc-bfx/dcgc-jupyter-rstudio:latest
Singularity Recipe
Bootstrap: shub
From: dcgc-bfx/dcgc-base-conda:0.1.1
%labels
Author fabian.rost@tu-dresden.de
Organisation DcGC
Version latest
%help
Start jupyter lab:
singularity run --writable-tmpfs --app jupyter library://fabianrost84/dcgc/single-cell.sif
Start rstudio server listening on port 8787:
singularity run --writable-tmpfs --app rserver library://fabianrost84/dcgc/single-cell.sif 8787
%files
files/jupyter_notebook_config.json /opt/conda/etc/jupyter/
files/rserver.conf /etc/rstudio/rserver.conf
%environment
DEBIAN_FRONTEND=noninteractive
%post
chmod -R a+w /opt
export PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
mamba install --quiet --yes \
ipykernel \
jupyter_nbextensions_configurator \
jupyterlab \
nodejs \
r-irkernel
# clean conda cache
mamba clean -ai --quiet --yes
# jupyterlab extensions
jupyter labextension install "@jupyterlab/toc"
# rstudio server
apt-get update --fix-missing -q
apt-get install -y -q \
gdebi-core \
uuid
wget --no-verbose https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.4.1106-amd64.deb
gdebi -q -n rstudio-server-1.4.1106-amd64.deb
rm rstudio-server-1.4.1106-amd64.deb
chmod -R a+rw /var/lib/rstudio-server
apt-get clean -q
rm -rf /var/lib/apt/lists/*
# for running rstudio server with conda R
git clone https://github.com/grst/rstudio-server-conda.git
chmod -R a+w /opt
####################
## rstudio server ##
####################
%apprun rserver
bash <<-EOF
source activate /opt/conda
/rstudio-server-conda/start_rstudio_server.sh "${@}"
EOF
#################
## jupyter lab ##
#################
%apprun jupyter
bash <<-EOF
source activate /opt/conda
jupyter lab --no-browser "${@}"
EOF
Collection
- Name: dcgc-bfx/dcgc-jupyter-rstudio
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/dcgc-bfx-dcgc-jupyter-rstudio-latest |
collection name | dcgc-bfx/dcgc-jupyter-rstudio |
branch | main |
tag | latest |
commit | b2e705533b18c9db0c89eb27e1991fcf24b7992c |
version (container hash) | 44d967178ec71f24281b9611c4909fb8868870425e86a9c6f34500c3502dc931 |
build date | 2021-04-12T08:52:34.024Z |
size (MB) | 1539.01171875 |
size (bytes) | 1613770752 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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