docker-rgriffin.md

In mar-esther23/rgriffin: Gene Regulatory Interaction Formulator For Inquiring Networks

rGriffin Docker Instructions

Running

1. Install docker in your system

2. Run the following command from the terminal, change mypassword for a password you select, and the path (/home/user/tmp/) to an existing path in you local file system, you can also change /home/rstudio/tmp to a different location but keep the base path /home/rstudio/

docker run --rm -e PASSWORD=mypassword -p 8787:8787 -v /home/user/tmp/:/home/rstudio/tmp stanmoon/rgriffin

The container will be removed when it exits, but this can be changed by removing de --rm option. See more options in the docker documentation.

1. Open browser at localhost:8787 and connect with the user rstudio and with the password you provided in step 2

Image Creation and Sharing

1. Install docker in your system

2. Run the following command from the terminal, change mypassword for a password you select, and the user path (/home/user/tmp/) to an existing path in you local file system you can also change /home/rstudio/tmp to a different location but keep the base path /home/rstudio/

docker run --rm -p -e PASSWORD=mypassword 8787:8787 -v /home/user/tmp/:/home/rstudio/tmp rocker/verse

1. Open browser (localhost:8787) and connect with the user rstudio y with the password you provided in step 2

2. Follow rGriffin installation instruction (do not stop the instance after you finish this step).

3. After successful instalation and testing of rGriffin, open a new terminal and obtain the container id of the rstudio instance by typing

docker ps

A message similar to the following will be printed in the terminal

CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES 3e4afb7d547c rocker/verse "/init" 21 minutes ago Up 21 minutes 0.0.0.0:8787->8787/tcp boring_cray In this case 3e4afb7d547c is the container ID, we will use this ID in the next step

1. Save the new image with the following command:

docker commit -m "rstudio with rGriffin package" 3e4afb7d547c rstudio_rgriffin

Here we have created a new image -m option gives a descriptive message, the name of the image in this case is rstudio_rgriffin, but another label can be selected.

1. connect to the new docker image using the name given in step 6

docker run --rm -e PASSWORD=mypassword -p 8787:8787 -v /home/user/tmp/:/home/rstudio/tmp rstudio_rgriffin

1. open the browser and verify that rGriffin is indeed installed and running.

2. login to docker hub

docker login -u dockeralias

1. tag the image to match your alias in docker hub

docker tag rstudio_rgriffin dockeralias/rgriffin

1. push the image to the server

docker push dockeralias/rgriffin

mar-esther23/rgriffin documentation built on May 29, 2021, 10:03 p.m.