README

This module is used to build and maintain a database of RNAseq tracks.

- The Mysql schema is in sql/tables.sql and documented in docs/rnaseqdb_doc.html
- The modules are in lib/
- Various scripts are in the scripts folder to:
  - Add species
  - Add RNA-Seq from SRA or from local files
  - Annotate the metadata (e.g. create groups of tracks)
  - Retrieve tracks

Special prerequisite:
* Bio::EnsEMBL::TrackHub from https://github.com/MatBarba/EGTrackHub
* Bio::EnsEMBL::ENA


INSTALL

Either put script in a dedicated dir and update PERL5LIB (lib/) and PATH (scripts/), or
install the package:

# Prepare and test
perl makeFile.PL
make
make test

# Install
make install

# Cleanup
make veryclean

NOTE1: even if you do not install the package, it is best to perform the 3 first
steps to check for dependencies and run the tests.

NOTE2: The tests mainly rely on an access to a database: rename
t/RNAseqDB/db_conf.example
to
t/RNAseqDB/db_conf
and change its content appropriately to be able to test properly.



To build the MANIFEST easily:
perl -MExtUtils::Manifest -e 'ExtUtils::Manifest::mkmanifest()'