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Update bioseg.rst
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Julie Sullivan committed Jan 6, 2015
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Range Queries (BioSeg)
===========
=================================

.. note::
Starting with InterMine 1.4 Bioseg is no longer required if you are using a Postgres version higher than 9.1.


Postgres 9.2 and higher
=======================
-------------------------------

InterMine now can perform range queries on location table taking advantage of Postgres built in ``int4range`` type.

Expand All @@ -18,7 +18,8 @@ New installations of Postgres may still need to install gist for the indexes to


Indexing
--------
~~~~~~~~~~~~~~

Performance is improved by creating an index of int4range(start, end) on the location table.

This is achieved in the post-process phase of the build of an InterMine (see :doc:`/get-started/tutorial/index`).
Expand All @@ -28,37 +29,38 @@ Please use the ``create-location-range-index`` post-process, which should replac
The ``create-overlap-view`` task will also detect whether built-in ranges are available and use them instead of bioseg for the overlappingfeatures view.

Postgres 9.1
=============
------------------

For Postgres 9.1 bioseg is still required. Here how to install it.

Prerequisites
-------------------
~~~~~~~~~~~~~~~~~~~~~~

Contrib software
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
^^^^^^^^^^^^^^^^^^^^^^^^^^^^

======== ==========================================
debian apt-get install postgresql-contrib-9.1
fedora yum install postgresql-contrib
======== ==========================================

Header files
~~~~~~~~~~~~~~
^^^^^^^^^^^^^^^^^^^^^^^^^^^^

======== ==========================================
debian apt-get install postgresql-server-dev-9.1
fedora yum install postgresql-devel
======== ==========================================

pg_config
~~~~~~~~~~~~~~
^^^^^^^^^^^^^^^^^^^^^^^^^^^^

======== ==========================================
debian apt-get install libpq-dev
======== ==========================================

Installation
------------------
~~~~~~~~~~~~~~~~~~~~~~

1. Download the bioseg tar from http://www.bioinformatics.org/bioseg/wiki/.
2. Untar the file, change to the created directory and run these commands
Expand All @@ -71,7 +73,7 @@ Installation
Create bioseg Type
----------------------
~~~~~~~~~~~~~~~~~~~~~~

You need to create the bioseg type in each database that is going to use it. If you create it in the `template1`, then all newly-created databases will have the bioseg type.

Expand All @@ -94,7 +96,7 @@ For each database, type:
$ psql (database) <bioseg.sql
Gist
=====
---------

We also need to create the default gist operators too, in order to have normal types in multi-column indexes.

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