Granatum is a graphical single-cell RNA-seq (scRNA-seq) analysis pipeline for genomics scientists.
Please Cite: Zhu, Xun et al. Granatum: A Graphical Single-Cell RNA-Seq Analysis Pipeline for Genomics Scientists. Genome Medicine 9.1 (2017)
You can use Granatum on our cloud instance running at http://granatum.dcmb.med.umich.edu/ or clone this repository and setup a server of your own locally or in the cloud.
Besides, we also have an updated version named GranatumX. You can also try GranatumX at http://garmiregroup.org/granatumx/app.
This should also mostly work for other targets
This should work on Google Cloud.
machine_setup.sh
(or run the commands individually)Rscript installDependencies.r
Rscript load_dependencies.r
git clone https://github.com/lanagarmire/granatum
npm install .
node app.js
sudo apt-get install libcap2-bin; sudo setcap cap_net_bind_service=+ep /usr/local/bin/node
sudo yum install libcap-devel; sudo setcap cap_net_bind_service=+ep /usr/local/bin/node
echo "R_MAX_NUM_DLLS=500" > ~/.Renviron