ucbd2k/nl_rnaseq repository overview

⁠Nl_rnaseq: Docker container for generating Neurolincs RNA-seq signature (Step-2) in RStudio

This docker container is developed to create Neurolincs RNA-seq level 4 signature data from level 3 counts data. The docker has been tested on Neurolincs level 3 data downloaded from Lincs data portal⁠. The docker has been tested for all of the on Linux (Ubuntu 14.04 and 16.04), macOS (10.11.6), and Windows (Windows 7 Enterprise).

⁠Installation of Docker

Ubuntu: follow the instructions⁠ to get Docker CE for Ubuntu.

Mac: follow the instructions⁠ to install the Stable verion of Docker CE⁠ on Mac.

Windows: follow the instructions⁠ to install Docker Tookbox⁠ on Windows.

⁠Download and run the docker container

To obtain the docker image and run the container,

[sudo] docker pull ucbd2k/nl_rnaseq:stable

Linux users may need to use sudo to run Docker.

To run the container execute the following command:

[sudo] docker run -d -p <an available port>:8787 ucbd2k/nl_rnaseq:stable

Typically one can use port 8787 if not already used by another application. In that case the commad is

[sudo] docker run -d -p 8787:8787 ucbd2k/nl_rnaseq:stable

First make sure that port 8787 is free to use for the rstudio, (Typically rstudio dockers run on this port, if this port is free ignore the rest of this section). You can stop and kill any othe docker containers on this port by

[sudo] docker stop <container ID> && docker rm <container ID>

To know the container ID run this command:

docker ps -a

To start an RStudio session, open a browser and type in the address bar <Host URL>:<available port as specified>. Enter rstudio for both username and password. For example http://localhost:8787 on Mac or Linux systems when 8787 port is used.

Host URL on Ubuntu and Mac is localhost, if accessed locally. On Windows, the IP is shown when Docker is launched by double-clicking the Docker Quickstart Terminal icon on desktop, or it can be obtained from the output of docker-machine ls in the interactive shell window.

⁠Execute the processing pipeline

After entering the rstudio environment, type the following command in the console:

source("process_neurolincs_data.R")

You can also open the R code by clicking the file named process_neurolincs_data.R from the files panel in the bottom-right of your window. Once you see the code appears in the top-left window, you can select the whole code and click Run at the top of your window.

You can run this pipeline for the given dataset (LDS-1398). The pipeline will generate the signature data and save the data as .csv file in the working directory.