SamTools service

The SamTools service allows the Grassroots Server to use the functionality provided by Samtools by Heng Li et al.. Currently it has the ability to retrieve a complete named scaffold from some sequence data.

Installation

To build this service, you need the grassroots core and grassroots build config installed and configured.

The files to build the SamTools service are in the build/<platform> directory.

Linux

Enter the build directory

cd build/linux

and create a user.prefs file.

cp example-user.prefs user.prefs

You will need to edit this file to configure where the SamTools dependencies are stored. The file content is similar to the following

#
# samtools dependencies
#
# Set this to where you have the htslib directory
# containing "include" and "lib" subdirectories.
export HTSLIB_HOME := $(DIR_GRASSROOTS_EXTRAS)/htslib

Adjust the HTSLIB_HOME to where you have htslib installed. You can then build the service by typing

make all

and then

make install

to install the service into the Grassroots system where it will be available for use immediately.

Configuration options

The service can be configured by a file with the same names in the config directory in the Grassroots application directory, e.g. config/SamTools service.

  • index_files: This is an array of objects with each consisting of two key-value pairs. Either option is sufficient when attempting to run the SamTools service.
    • Blast database: The name of the Blast database file that SamTools can run against.
    • Fasta: The Fasta file that the Blast database was generated from.