INSTALL.md

Installation

Skip this step if you've created a server instance with Caper's GCP startup script. Install Caper and configure Caper for GCP. Follow instrutions in Caper's conf ~/.caper/default.conf (or /opt/caper/default.conf).

$ pip install caper
$ caper init gcp

Install dependencies.

sudo apt-get install trimmomatic -y # version 39
sudo apt-get install samtools python3-deeptools -y

# install singularity on Ubuntu 20.04
# See https://neuro.debian.net/install_pkg.html?p=singularity-container for other Ubuntu OS
wget -O- http://neuro.debian.net/lists/focal.us-ca.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
sudo apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
sudo apt-get update && sudo apt-get install singularity-container -y

And then run ./install.sh.

Temp directory permission

Grant all permissions to anyone on the instance.

$ cd ihec-processing # go to git directory
$ chmod 777 -R .
$ sudo setfacl -R -d -m u::rwX .
$ sudo setfacl -R -d -m g::rwX .
$ sudo setfacl -R -d -m o::rwX .

Example

See this