DoBlastzChainNet.pl
Prerequisites
This discussion assumes you are familiar with Unix shell command line programming and scripting. You will be encountering and interacting with csh/tcsh, bash, perl, and python scripting languages. You will need at least one computer with several CPU cores, preferably a multiple compute cluster system or equivalent in a cloud computing environment.
Parasol Job Control System
The scripts and programs used here expect to find the Parasol_job_control_system in place and operational.
Install scripts and kent command line utilities
This is a bit of a kludge at this time (April 2018), we are working on a cleaner distribution of these scripts. As was mentioned in the parasol job control system setup, the kent command line binaries and these scripts are going to reside in /data/bin/ and /data/scripts/. This is merely a style custom to keep scripts separate from binaries, this is not strictly necessary.
mkdir -p /data/scripts /data/bin git archive --remote=git://genome-source.soe.ucsc.edu/kent.git \ --prefix=kent/ HEAD src/hg/utils/automation \ | tar vxf - -C /data/scripts --strip-components=5 \ --exclude='kent/src/hg/utils/automation/incidentDb' \ --exclude='kent/src/hg/utils/automation/configFiles' \ --exclude='kent/src/hg/utils/automation/ensGene' \ --exclude='kent/src/hg/utils/automation/genbank' \ --exclude='kent/src/hg/utils/automation/lastz_D' \ --exclude='kent/src/hg/utils/automation/openStack'