Description Usage Arguments Details Value Author(s)
View source: R/oop_functions.R
Many programs are needed for the run of virDisco. Here the program executables are defined.
1 2 3 | 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)
|
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 |
See https://github.com/jkruppa/virDisco for a list of program sources.
program_list
Jochen Kruppa
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