Biopieces

Description

biopieces website  

The Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each performing one specific task: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services. The Biopieces are executed in a command line environment where the data stream is initialized by specific Biopieces which read data from files, databases, or web services, and output records to the data stream that is passed to downstream Biopieces until the data stream is terminated at the end of the analysis as outlined below:

Environment Modules

Run module spider biopieces to find out what environment modules are available for this application.

System Variables

• HPC_BIOPIECES_DIR - installation directory
• HPC_BIOPIECES_BIN - executable directory
• BP_DIR - biopieces directory
• BP_DATA - biopieces data directory
• BP_TMP - biopieces tmp directory
• BP_LOG - biopieces log directory

Additional Information

The software requires users to create the BP_DATA, tmp, and BP_LOG directories in your working path. After loading the module use the following command:

mkdir $BP_DATA $BP_TMP $BP_LOG