In JovingeLabSoftware/ExpSpect: Calculate protein specific biases in gene expression

Overview of Approach

We leverage the excellent work of the rocker-org team.

Developers will need to be on a machine with sufficient storage space (>120 GB) and have Docker installed installed.

AWS Configuration

AWS has proven to be the easiest platform for working with LINCS data.

Starting on a fresh Ubuntu spot instance with attached storage instance (we usually use 200 GB EBS).

The following commands were adopted from the AWS docs and show the basic workflow of mounting an attached EBS volume to /data/ on our working instance.

# see if we need to create file system + create it
sudo file -s /dev/xvdf
sudo mkfs -t ext4 /dev/xvdf

# create mount point and mount
sudo mkdir /data
sudo mount /dev/xvdf /data

# install docker
wget -qO- https://get.docker.com/ | sh

# run our container in daemon mode
sudo docker run -d --name rstudio -v /data:/data rocker/rstudio

JovingeLabSoftware/ExpSpect documentation built on May 8, 2019, 4:38 p.m.