Step 1: Get the tools

The tools needed for this workflow are:
Picard: http://picard.sourceforge.net/
Samtools: http://samtools.sourceforge.net/
Burrows-Wheeler Aligner: http://bio-bwa.sourceforge.net/
GATK: https://www.broadinstitute.org/gatk/download
Cuneiform: https://github.com/joergen7/cuneiform

Step 2: Get the files

Reads: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG00096/sequence_read/
Known variants: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20110521/ALL.chr22.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz
Training data: http://gatkforums.broadinstitute.org/discussion/1215/how-can-i-access-the-gsa-public-ftp-server

Step 3: Prepare the callers

Make the tools callable from your path. Picard and GATK need a bit of an extra handling.
GATK supports no Java 1.8 at the moment, if your standart version is 1.8, you need to call the GenomeAnalysisTK.jar with a prior version, best would be 1.7.
Create a bash script for picard, calling a jar in the form of: picard-tools-1.114/picard-tools-1.114/$1
This will enable you to give the desired jar as first argument after the call.

Step 4

Navigate to the folder where all the data-files are stored and start cuneiform there.

Step 5: Run the workflow.

Good luck!