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.
- Create Ubuntu 18 VM
- SSH to VM.
- Run
machine_setup.sh(or run the commands individually) - Run
Rscript installDependencies.r - Verify that worked with
Rscript load_dependencies.r - Do a
git clone https://github.com/lanagarmire/granatum - cd granatum1/server
npm install .node app.js- Make sure both Google Firewall and Ubuntu Firewall are open for Granatum ports
- To run on port 80 you need to allow node to run on privileged ports:
- Ubuntu:
sudo apt-get install libcap2-bin; sudo setcap cap_net_bind_service=+ep /usr/local/bin/node - Fedora:
sudo yum install libcap-devel; sudo setcap cap_net_bind_service=+ep /usr/local/bin/node - Increase R's default R_MAX_NUM_DLLS
echo "R_MAX_NUM_DLLS=500" > ~/.Renviron