inst/RNA_git/README.md

In amcdavid/GeneseeBulk: Pipeline, analysis functions and markdown templates for bulk RNAseq

{{Genesee.title}} {{Genesee.type}}

Developer instructions

1. Consider having ssh-agent cache credentials. eval ssh-agent; ssh-add
2. Clone this repository
3. On bluehive, start rstudio-server rstudio-server.sh -S init-Rstudio-server.sh -- -t 0-6 --mem-per-cpu=32gb # modify node needs
4. proto_driverR.R is just a list of commands used to generate this repo
5. Modify scripts, copying changes that are generalizable back up to {{Genesee.template.package}}/inst/{{Genesee.type}}_markdown or add functions in {{Genesee.template.package}}/R
6. Big intermediate files that shouldn't be version-controlled can go in scratch/. If they might be used by investigators, they should go in refined/ (which uses git LFS to avoid bloating the repo).
7. Follow Git-lfs instructions to commit into refined/ other large objects. (It doesn't work from RStudio server, anyways.)

Investigator instructions (WIP)

It is intended that this repo will serve as portal for investigators.

For single cell data, we'll describe

• how to get the cloupe data
• how to run iSEE locally

amcdavid/GeneseeBulk documentation built on March 26, 2022, 4:58 a.m.