TransAtlasDB

Introduction

TransAtlasDB is an integrated database system from transcriptome analysis data.

This is the GitHub repository for the documentation of the TransAtlasDB software.

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TransAtlasDB main package

The TransAtlasDB toolkit is written in Perl and can be run on diverse hardware systems where standard Perl modules and the Perl-DBD module are installed. The package consist of the following files:

• INSTALL-tad.pL: install TransAtlasDB system.

• connect-tad.pL: verify connection details or create connection details (used only when requested).

• tad-import.pl: import samples metadata and RNAseq data into the database.

• tad-interact.pl: interactive interface to explore database content.

• tad-export.pl: view or export reports based on user-defined queries.

• other folders:

  • schema : contains the TransAtlasDB relational database schema.
  • example : contains sample files and templates.
  • lib : contains required Perl Modules.
  • web : TransAtlasDB web portal ( is visible after executing INSTALL-tad.pl )

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TransAtlasDB installation

• Requirements:

  • Operating System :

    • Linux / Mac (tested and verified)

  • Databases :

    • MySQL
    • FastBit

  • Perl Modules needed :

    • DBD::mysql
    • Spreadsheet::Read
    • Spreadsheet::XLSX
    • Text::TabularDisplay
    • Sort::Key

• Quick Guide:

  • To install [RECOMMENDED: with root priviledges]

   INSTALL-tad.pl -password <mysql-password>
  

  • More details and instructions are provided at https://modupeore.github.io/TransAtlasDB/tutorial.html

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TransAtlasDB web portal

• Requirements:

  • Requirements in the above section (TransAtlasDB installation).
  • PHP (at least version 5.5.38)
  • Apache (at least version 2.4.18)

• Guide:

  • After installation of the TransAlasDB databases and dependencies (as show above). The web folder is provided and should be moved to your localhost or apache location.

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If you have questions, comments and bug reports, please email me directly. Thank you very much for your help and support!