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.
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.
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.
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.
-
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.