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Biopipe Install Directions
o System Requirements and Inatallation
-Tested only Linux, Mac OS X and Alpha OSF
-perl 5.6 or latter
-mySQL database
The bioperl-pipeline relies on a MySQL database for its job management and tracking.
This allows persistence of most operations inherent to the pipeline, which
in turn allows the pipeline to restart seemlessly even after an abrupt halt due
to some system failure (e.g. network problems, power cut, and so on). Obtain MySQL
from and refer to the MySQL documentation for installation
instructions. Once MySQL is installed and running you can create the bioperl-pipeline
-Load Sharing Software
The bioperl-pipeline can be run locally on your own machine without load-sharing
software and will still manage the logic and workflow of your analysis runs. However
to truly harness the bioperl-pipeline's power you will need either:
1) LSF (Load Sharing Facility) a commercial package, but very cheap or free for small academic setups.
2) PBS (Portable Batch System) Freely Available for the Open PBS version.
* We are currently looking for parties interested in provding a port to Sun Grid Engine.
Do contact us to let us know!
Without load-sharing you will be running your jobs in 'local' mode.
Each job is then run sequentially but this is not recommended for high throughput analysis.
-Bioperl Packages
bioperl-live bioperl-run-release-1-2-0 or later
bioperl-run bioperl-run-release-1-2-0
bioperl-pipeline bioperl-run-release-1-2-0
recommended: bioperl-db
The packages are available from CVS using the following commands:
cvs -d checkout -r bioperl-run-release-1-2-0 bioperl-live
cvs -d checkout -r bioperl-run-release-1-2-0 bioperl-run
cvs -d checkout -r bioperl-run-release-1-2-0 bioperl-pipeline
password is 'cvs'
More Info: http:://
Install the bioperl-pipeline package in the standard way:
>cd bioperl-pipeline
>perl Makefile.PL
Before doing make test, ensure that you modify the following files to reflect
your system specifics:
1) bioperl-pipeline/t/BiopipeTestDB.conf
2) bioperl-pipeline/Bio/Pipeline/
In particular, ensure that your mysql configurations are correct.
Having done, so, you may continue :
>make test
>make install
To create a Mysql pipeline database:
>mysqladmin -u root create biopipe
To create the pipeline database tables:
>cd bioperl-pipeline
>mysql -u <user> biopipe < sql/schema.sql
Biopipe databases are automatically created when pipelines are run(mysql configuration
read from , so this is a useful test but not necessary for installation.
Although recommended, you do not need to install the packages. You may simply put them into
a directory and point to them in your PERL5LIB environment variable like so:
setenv $CVSPATH "/Users/shawn/cvs_src"
setenv PERL5LIB "$CVSPATH/bioperl-pipeline:$CVSPATH/bioperl-run:$CVSPATH/bioperl-1-2-1:$CVSPATH/bioperl-db-1-1-0:
For detailed instructions on installing Bioperl please refer to the INSTALL document
in bioperl-live or in the latest Bioperl release. This document discusses issues like
installation into non-standard locations or how to install a Perl package if you don't
have root access (Unix).
Installation of Bioperl on Windows is discussed in the INSTALL.WIN document in bioperl-live
or in the latest Bioperl release.
- Perl Packages
available at
XML::SimpleObject - required
XML::Parser or XML::SAX::PurePerl - either one is required.
Note XML:Parser requires Expat installed and some parties have had problems
getting this installed. As an alternative solution, XML::SAX::PurePerl doesn't
require Expat and this is a viable alternative. The latter is of course slower
but XML parsing only takes up a minute portion of biopipe and thus
speed here is not a consideration. Biopipe will default to XML::Parser. If not
installed, it will check for XML::SAX::PurePerl.
Data::ShowTable - optional
This package is used by the job_viewer script in bioperl-pipeline/scripts that
provides a nice interface for querying the various job status in the pipeline.