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1. User Installation

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arnald edited this page Dec 2, 2016 · 2 revisions

aRNApipe User Installation

This section provides a guide to configure an user account to use aRNApipe.

aRNApipe base path

A base pipeline path (i.e. the directory where the pipeline is installed) must be provided by the administrator and will be refered as $BP. The base path folder contains the main pipeline scripts.

Creating the links to the main scripts

In order to make the calls to the pipeline easier, the use of an alias for the main pipeline scripts is highly recommended. These scripts are:

  • $BP/aRNApipe.py: Main pipeline application.
  • $BP/spider.py: Add-on module for gathering the results generated by the main application and creating a web report.

The alias to these scripts can be generated with the following commands:

alias aRNApipe='python $BP/aRNApipe.py'
alias spider='python $BP/spider.py'

To make these alias permanent, the user should add the commands above to the end of its ~/.bashrc file. To make these alias available in the current shell source the ~/.bashrc file:

source ~/.bashrc

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