set_program_list: Path to the external program executables

In jkruppa/virDisco: Modules for a viral detection pipeline

Description

Many programs are needed for the run of virDisco. Here the program executables are defined.

Usage

set_program_list(bowtie_dir, pauda_dir, star_dir, bowtie_build_dir,
  pauda_build_dir, samtools_dir, trimmomatic_dir, pandaseq_dir, seqtk_dir,
  blastn_dir, ete3_dir)

Arguments

bowtie_dir	Path to Bowtie2 DNA mapper
pauda_dir	Path to PAUDA - a poor man's BLASTX
star_dir	Path to Star mapper [optional]
bowtie_build_dir	Path to the Bowtie2 build dir
pauda_build_dir	Path to the Bowtie2 build dir for PAUDA
samtools_dir	Path to Samtools
trimmomatic_dir	Path to Trimmomatic
pandaseq_dir	Path to PANDAseq
seqtk_dir	Path to Seqtk
blastn_dir	Path to the BLAST executables
ete3_dir	Path to the ETE Toolkit
star_build_dir	Path to the Star build dir

Details

See https://github.com/jkruppa/virDisco for a list of program sources.

Value

program_list

Author(s)

Jochen Kruppa

jkruppa/virDisco documentation built on May 3, 2019, 7:05 p.m.