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 to keep them separate.

 mkdir -p /data/scripts /data/bin
 chmod 755 /data/scripts /data/bin

 rsync -a rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/ /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'

PATH setup

Add or verify the two directories /data/bin and /data/scripts are added to the shell PATH environment. This can be added simply to the .bashrc file in the your home directory:

echo 'export PATH=/data/bin:/data/scripts:$PATH' >> $HOME/.bashrc

Then, source that file to add that to this current shell:

. $HOME/.bashrc

Verify you see those pathnames on the PATH variable:

echo $PATH
/data/bin:/data/scripts:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/centos/.local/bin:/home/centos/bin

This entire discussion assumes the bash shell is the user's unix shell.

Working directory hierarchy

It is best to organize your work in a directory hierarchy. For example maintain all your genome sequences in:

 /data/genomes/
 /data/genomes/hg38/
 /data/genomes/mm10/
 /data/genomes/dm6/
 /data/genomes/ce11/
 ... etc ...

Where those database directories can have the 2bit files, chrom.sizes, and track construction directories, for example:

 /data/genomes/dm6/dm6.2bit
 /data/genomes/dm6/dm6.chrom.sizes
 /data/genomes/dm6/trackData/

Such organizations are a personal preference custom. However you do this, keep it consistent to make it easier to use scripts on multiple sequences.