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MPC statistical pipeline docker container

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Hamed Ha edited this page Aug 16, 2020 · 1 revision

IMPC statistical pipeline docker container

The IMPC statistical pipeline (IMPC-SP) workflow is containerised and available from the docker hub,

The docker image contains all requirement for running the IMPC statistical pipeline including R and package dependencies.

How to run the IMPC-SP docker image?

To run the container you should first download the image from docker hub by executing the command docker pull hamedhm/impc_stats_pipeline or following the instruction below in your favourite terminal,

  1. docker pull hamedhm/impc_stats_pipeline
  2. docker images
  3. docker run -it --entrypoint /bin/bash <IMGE_ID from the output of the command above>

The latest command opens an interactive shell that you can run R by simply executing the R command.

Frequently asked questions

Here we answer some of the frequency asked questions.

  • What is Docker container?
    • Docker container is an easy and lightweight approach to containerize and ship software. See the home page for more details.
  • Where are the IMPC-SP on Github?
  • How long normally the IMPC-SP takes to complete?
    • This depends on the LSF cluster and the available resources. Setting the EMBL-EBI LSF cluster as a reference, the whole process takes from 2 days to 4 days.
  • How to run the One-line-execution of the IMPC-SP under different settings?
    • This requires changing the setting in the DRrequiredAgeing package, precisely the scripts in here. One can fork the repository and change the settings, then update the package from GitHub using devtools::install_github command in R.
  • How to ask for help?
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