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Lucie Hutchins edited this page Dec 26, 2019 · 76 revisions

Biocore Package Downloads Repos

A repository to create automations that download and Install external bioinformatics packages. For each installed package, this tool can be setup to run an automation that checks if a new version of the tool is available. As soon as it detects a new release of the tool, the automation will download and install it locally.

What It Does

For each package installed,the automation creates a root directory that is the name of the tool in the path defined by our standards - The path is set in the main Configuration (EXTERNAL_SOFTWARE_BASE).

Under each installed tool root directory, you will find:

  1. A file (current_release_NUMBER) that stores the latest version of this tool.
    this file is updated by getToolVersion.sh/setToolVersion.sh scripts
  2. A directory for each version of this tool installed
  3. A symbolic with this tool name that points to the latest version installed

Getting Started

Dependencies

Assuming a Linux system , on the command line run the 'which' command with any of the following programs as argument to check it if it's installed.

  1. git (tested with version 1.8.3.1)
  2. sh
  3. wget (tested with GNU Wget 1.14 built on linux-gnu)
  4. make
  5. cmake (version 3.5 or higher)
  6. tar
  7. locate
  8. pip
  9. virtualenv
  10. unzip
  11. curses, ncurses
 sudo yum install ncurses-devel ncurses

R dependencies 12. libgfortran, gcc-gfortran, gcc-objc

 sudo yum install  gcc-gfortran libgfortran gcc-objc
  1. readline, readline-devel
sudo yum install readline readline-devel
  1. pcre, pcre-devel (version >= 8.20)
 sudo yum install  pcre pcre-devel
  1. tbb,tbb.i686, tbb-devel (bowtie uses)
sudo yum install  tbb tbb.i686 tbb-devel
  1. gnu plot
sudo yum install gnuplot

For example: to check that git is installed run: which git

Repos Organization

Tools

Each tool is a sub-directory that contains:

  1. a configuration file
  2. a dependencies file
  3. an install script (only for some tools)

The name of each tool is all in lowercase and matches the name of the install root directory of the tool. Different versions of each tools are installed under the same root directory and the name of the root directory is the same as the tool's name.

Main Scripts and Config

In addition to tool directories, the following are found under the package's root.

Global config and setup

Used to get/set the version of the tool to install - Run before the package manager script

Package Manager Automation Trigger

Package Manager

Used by the Package Manager to download/export packages

Package Manager Helpers -

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