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bioperl-db INSTALLATION
INSTALL BIOPERL FIRST
You need at least the corresponding version of Bioperl. Since this
is bioperl-db 1.5.2, you will need bioperl 1.5.2 or later.
Installation instructions are here:
http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix
THEN INSTALL BIOSQL
The bioperl-db package is designed to work with the BioSQL database.
Install the BioSQL package by following the instructions in its
INSTALL file. You can obtain the BioSQL package at www.biosql.org.
BioSQL requires a relational database, either Mysql, Oracle, or
PostgreSQL.
INSTALL BIOPERL-DB USING CPAN
Enter the CPAN shell:
perl -e shell -MCPAN
Now install:
cpan>install CJFIELDS/BioPerl-DB-1.006900.tar.gz
MANUALLY INSTALL BIOPERL-DB
Use this URL to download the archive:
https://github.com/bioperl/bioperl-db/archive/master.zip
Then:
>unzip master.zip
>cd bioperl-db-master
Issue the following command from within bioperl-db/:
>perl Build.PL
You can run regression tests and install bioperl-db using the
following commands:
>./Build test
>./Build install
NOTE: bioperl-db tests require that the BioSQL database you configure
does NOT have the NCBI taxonomy loaded. Also, the './Build install' step
may require that you have root privileges.
INSTALLING bioperl-db ON WINDOWS
The following page on the BioPerl website has up-to-date
instructions on how to install bioperl-db on Windows:
http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
(the instructions are aimed at bioperl-core, but apply
equally to bioperl-db)
LOAD THE NCBI TAXONOMY
You should pre-load the NCBI taxonomy database using the
scripts/load_ncbi_taxonomy.pl script in the BioSQL package.
Otherwise you will see errors from mis-parsed organisms when you
attempt to load sequences.
LOAD SEQUENCE DATA
Most people will want to load sequence data into their BioSQL
databases. Use scripts/biosql/load_seqdatabase.pl in the bioperl-db
package to load sequences from sequence files. Do:
>perldoc scripts/biosql/load_seqdatabase.pl
or
>scripts/biosql/load_seqdatabase.pl --help
for more information.
This script has many options to flexibly deal with various update
scenarios. Do read the POD before running an update.
LOAD ONTOLOGIES
Use scripts/biosql/load_ontology.pl in the bioperl-db
package to load ontologies from flat files. Do:
>perldoc scripts/biosql/load_ontology.pl
or
>scripts/biosql/load_ontology.pl --help
for more information.
This script has many options to flexibly deal with various update
scenarios. Do read the POD before running an update. Also, some
ontologies maintain obsoleted terms, for instance the Gene
Ontology. Read the POD for possible options to deal with obsoleted
terms; this is relevant even when you load the ontology the first
time, as you may choose to keep obsoleted terms out of the database
from the start.
FEEDBACK
Write down any problems or praise and send them to
bioperl-l@bioperl.org ;-)
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