Running the TPP docker image

From SPCTools

Contents 1 Overview 2 Downloading spctools/tpp docker image 3 Verifying that the image has been downloaded 4 Running a specific TPP program from the docker image 5 Running the TPP gui via docker 6 Checking to make sure the docker is running 7 Obtaining a copy of the default parameter files

Overview

The docker system allows the distribution of pre-built computational units called images, which can be run on any system with the docker software installed. The spctools/tpp image is built on the BioContainers ubuntu image, and uses many of the BioContainers conventions. On some systems you may have to run these commands using sudo, a mechanism for elevating user privileges for specific tasks. The initial download described below will be relatively slow the first time it is run, since most if not all the 'layers' will have to be downloaded. Subsequent invocations will generally be much faster.

Downloading spctools/tpp docker image

As mentioned above, this may be slow the first time it is run. Subsequent runs should be considerably faster. The example below shows a pull of the latest (default) version, you can also specify a specific version if desired.

docker pull spctools/tpp
 Using default tag: latest
 Trying to pull repository docker.io/spctools/tpp ... 
 latest: Pulling from docker.io/spctools/tpp
 Digest: sha256:686e9cc696fcbfd118a1ded28ae2d31218cbddd0daed68ac811400cc8833fa95
 Status: Image is up to date for spctools/tpp:latest

Verifying that the image has been downloaded

To verify that you've successfully downloaded the image, you can use the images command below, and hopefully see spctools/tpp entry(s):

 docker images 
  REPOSITORY                          TAG                 IMAGE ID            CREATED             SIZE 
  spctools/tpp                        latest              ebf55696681a        24 hours ago        3.2GB 
  spctools/tpp                        version5.2          ebf55696681a        24 hours ago        3.2GB 

Running a specific TPP program from the docker image

If you want to run a specific program, e.g. comet, from the tpp installation, you can invoke it along with any arguments as illustrated below:

'docker run spctools/tpp  comet -p
  Created:  comet.params.new 

Running the TPP gui via docker

To run the TPP as a server running on host myhost, you can invoke the following command (linux syntax):

 docker run -dit --user=root -p 10401:10401 -v /tmp/dmz/:/data/ spctools/tpp   
   350dc6eaafe113186c2ec23810bdbc442347a86c2632284435a4b6b713013771 

This will start a container running a web server from the spctools/tpp image, map port 10401 on the local machine (e.g. myhost) to the default webserver port on the container to enable access, and map a directory of your choosing (/tmp/dmz/ in this case) to /data/, the root directory for files in the tpp gui. This will give you access to your data in the tpp gui.

Checking to make sure the docker is running

 docker  ps 
  CONTAINER ID        IMAGE               COMMAND                  CREATED             STATUS              PORTS                      NAMES 
  350dc6eaafe1        spctools/tpp        "/bin/sh -c 'apache2…"   3 seconds ago       Up 1 second         0.0.0.0:10401->10401/tcp   suspicious_kilby 

You should see at least one spctools/tpp container running. To use the UI, direct your browser to the URL http://myhost:10401/tpp/cgi-bin/tpp_gui.pl where myhost is the network name of your computer (can also be IP address) You should be prompted to log in as user guest (password is guest)

Obtaining a copy of the default parameter files

There is directory of default parameter files included in the docker image. To download this directory to your local system (for example into the directory that you will mount in the tpp gui example above, you would run:

 docker run -v /tmp/test/:/data/  spctools/docker cp -R /usr/local/tpp/params /data/