testSeqbox: Testing the SeqBox basic installation

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

Testing the SeqBox basic installation

Description

This function executes a set of scripts to check if SeqBox installation is OK. It requests the existence of the following folders: /data/genomes, /data/scratch, /data/tests. /data/genomes folder must contain the following folders: hg38star mm10bwa mm10star

Usage

testSeqbox()

Value

testSeqBox.out file containing the results of the tests

Author(s)

Raffaele Calogero

Examples

## Not run: 
    #downloading in /data/genomes
    setwd("/data/genomes")
    system("wget http://130.192.119.59/public/hg38star.tar.gz")
    system("wget http://130.192.119.59/public/mm10star.tar.gz")
    system("wget http://130.192.119.59/public/mm10bwa.tar.gz")
    system("wget http://130.192.119.59/public/hg38salmon.tar.gz")
    system("gzip -d *.gz")
    system("tar xvf *.tar")
    setwd("/data/")
    system("wget http://130.192.119.59/public/tests.tar.gz")
    system("gzip -d tests.tar.gz")
    system("tar xvf tests.tar")
    system("rm tests.tar")
    #running test SeqBox
    library(docker4seq)
    testSeqbox()


## End(Not run)

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.