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Overview

Biopieces is a collection of ruby- and perl-based tools that can be used by bioinformaticians to perform essential utility functions on their data right out-of-the-box, or may be patched together in a pipeline.

In order to use Biopieces correctly, there are a couple of essential configuration steps that must be performed first.  These are covered in the following section(s).

Vmatch Group

Biopieces utilizes several external third party applications, including Vmatch, which are auto-loaded when the main "biopieces" module is loaded.  Use of Vmatch on the HPCC is restricted due to licensing requirements.  In order to load the default "biopieces" module, users must first read and accept Vmatch licensing agreement, and then acknowledge license by filing an HPCC licensing request.

Once you have been added to the Vmatch group, you should be able to load Biopieces and utilize its various tools:

 

module load biopieces

 

Configuration

Biopieces expects the user to create a couple of subdirectories in their home directory space, and to additionally define the location of these directories.

First, create the following:

 

mkdir ~/BP_DATA
mkdir ~/BP_LOG
chmod -R 755 ~/BP_DATA
chmod -R 755 ~/BP_LOG

 

Next, modify your ~/.bashrc file to add the following lines:

 

# >>>>>>>>>>>>>>>>>>>>>>> Enabling Biopieces <<<<<<<<<<<<<<<<<<<<<<<
export BP_DATA="/mnt/home/yourUID/BP_DATA"
export BP_TMP="/tmp"
export BP_LOG="/mnt/home/yourUID/BP_LOG"
# >>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

 

You will need to replace "yourUID" with your actual UID, and, ensure that the locations of the various directories are set correctly to your liking/needs.

Once your modified ~/.bashrc file has been modified, it must be "sourced" either manually or by logging-out and back in again.  To use Biopieces immediately without logging out and in again, you can use the following:

 

source ~/.bashrc

 

Once these steps are complete, you should be able to use Biopieces.

Tools

Users can get a list and summary of the available Biopieces by using the following command:

 

module load biopieces
list_biopieces

 

More Information