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Installation and Dependencies

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MiguelJulia edited this page Jun 7, 2019 · 5 revisions

Installation

PlasmidID needs all scripts located in /bin folder to be in the PATH. In order to do so, you need to add the following command to .bashrc file, normally located in /home/$USER/.bashrc:

export PATH=$PATH:/PATH/TO/PPLASMIDID/plasmidID/bin

In order to execute it, user needs to install all dependencies and execute plasmidID.sh with the required parameters.

In order to download plasmidID just clone the repository.

Hardware and software dependencies

Software dependencies

You will need the following software:

All these dependencies must be included in your $PATH for the pipeline to work without editing the code.

Hardware and configuration

This pipeline has been run and tested with Centos 6.7

  1. Home

  2. Installation and Dependencies

  3. Plasmid Database

  4. Execution

  5. Understanding the image: track by track

  6. Summary table and summary image

  7. How to chose the right plasmids

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