(1) Install prerequisite software or make sure they are already on your system.
The 3.1.1 version:
* Updated from DANPOS2 to run with updated packages:
* Python 3.7.6
* R 4.0.1
* samtools 1.7
* htslib 1.7
Thanks to Samantha Klasfeld from the Wagner lab at the University of Pennsylvania for contributing to the update
The 2.2.2 and earlieer versions:
R version 2.9.1.
Python 2.7.9, rpy2 2.6.0, numpy 1.5.0.
Samtools 0.1.7 (only when input data is in sam or bam format)
Memory ~ (genome_size/step_size) x ( replicate_count + max(2, comparison_count) ) x 8bytes.
(2) download the latest DANPOS version.
(3) extract DANPOS files on your server, e.g.:
tar -xvzf danpos-2.2.2.tgz
(4) go to the DANPOS directory, e.g., danpos-2.2.2, and run the command line below:
python danpos.py -h