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

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 scptools/tpp image is built on the biocontainer ubuntu image, and uses many of the bioC 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

If you want to run a specific program, e.g. comet, from the

1. 1. command of choice, e.g.

[sudo] docker run spctools/tpp comet -p

Created:  comet.params.new

1. 1. To run the TPP as a server running on host myhost, you can invoke the
   2. default command below. Note that we've mapped ports, and also mounted
   3. a local directory on /data/ in the docker container.

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

1. 1. You can check to make sure the docker is running

[sude] 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

1. 1. To use the UI, direct your browser to the URL http://myhost:10401/tpp/cgi-bin/tpp_gui.pl

1. 1. If you would like some default params files, you can cd to the DMZ dir above and exec:

wget /net/dblocal/wwwspecial/peptideatlas/tmp/params.tgz tar xvfz params.tgz rm -f params.tgz