hasihays / granatum

Granatum

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)

Try Granatum

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.

Setting up a Granatum1 Server on Google Cloud

This should also mostly work for other targets

This should work on Google Cloud.

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