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Programmatic Structure of the PLAS Pipeline

Overview

This series of scripts involves subscripts (often Perl), intermediate files, and scripts that call other scripts.

As such, this document is intended to clarify each programmatic step, parameter, dependency, and output of each script and subscript, beginning with the setup script.

There is an "all in one" bash script that involves blocking waits with afterok to run the scripts in order 01.PLAS.sh.

Script files are located in the plain PLAS directory and the Perl, Python, and R subscripts called by the main bash scripts are located in the 00.script directory.

00 setUp.sh

Summary

Creates the directories and subdirectories used in the pipeline.

Creates

Creates following directory structure (there are some inconsistent numbers and it also looks like the used the same folder mames if they were shared by a process, likely due to a calling Perl script):

00.script
01.data
|_00.PriorData
|_01.Fastq
|_03.MCL
    |_01.blast
    |_02.mcl
|_04.GeneOfInterest
|_05.SplitGenes
    |_01.Protein
        |_run.0
    |_02.Transcript
        |_run.0
    |_03.Full.Length
|_06.TargetTranscriptome
03.blast
|_03.bowtie.nucl
04.retrieve.reads
|_03.bowtie.nucl
06.assembly
|_03.bowtie.nucl
07.map.back
|_02.blastn
|_03.bowtie.nucl
08.full.length
09.fulllength.bowtie
10.unmappedreads.trinity

Calls

N/A

01 PLAS.sh

This is the master script that calls the other scripts using the Sapelo2 blocking wait afterok, which waits for a process to terminate before proceeding.

02.preRun.sh