Once downloading the tools, type chmod a+x irtools.osx or chmod a+x irtools.centos to change permission of this tools to execute the tool,
Type ./irtools.osx or ./irtools.centos, you get this
Program: irtools (Tools for analyzing CDR3 sequence data)
Version: 0.01
Usage: irtools -c parameter_file
A typical parameter_file looks like the following
#this line will be ignored
out_prefix=Prefix #entry after this pound sign will be ignored
cdr3_file=cdr3_file.txt
hla_file =hla_file.txt
refer_file=ref_file.txt
v_usage_freq_file=ref_V.txt
cdr3_length_freq_file=ref_L.txt
local_min_pvalue=0.001
p_depth = 1000
global_convergence_cutoff = 1
simulation_depth=1000
kmer_min_depth=3
local_min_OVE=10
algorithm=GLIPH2
all_aa_interchangeable=1
Please check the demo for input files' descriptions