configureArgs

# This file is used to configure default parameters of neoantigens computation
# Please change the content following the provided format
# If you want help, free to send email to <wangshx@shanghaitech.edu.cn> or open an issue at <https://github.com/ShixiangWang/Variants2Neoantigen/issues>

####### <<<<<< Location of Files
CACHE_VEP=/public/data/.neopip/vep/                                           # directory path of ensembl vep cache
PATH_FASTA=/public/data/.neopip/vep/homo_sapiens/91_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa           
                                                            # path of reference fasta file
iedb=~/Variants2Neoantigen/data/iedb/iedb.fasta             # iedb database used for blastp

####### <<<<<< Location of Softwares, python environment and input arguments
py_env=/public/data/.neopip/miniconda/                                                # python environment, which can run pvacseq 
py2_env=/public/data/.neopip/miniconda/envs/py27     # python2.7 

maf2vcf=maf2vcf.pl      # path of maf2vcf.pl script
PATH_VEP=/public/data/.neopip/miniconda/share/ensembl-vep-96.0-0/           # directory path of ensembl vep software
PATH_VEP_PLUGINS=~/VEP_plugins    # directory path of ensembl vep plugins
PATH_MHC=/public/data/.neopip/iedb                   # directory path of iedb local installation
vep_run=$PATH_VEP/vep
##vep_filter=$PATH_VEP/filter_vep

assembly_version="GRCh37"                               # genome build version, must be consistent in the analysis
method="NetMHC"                                         # multiple methods separated by space, like "NetMHC PickPocket NetMHCcons NNalign", but multiple method is not recommend
epitope_len="9"                                         # multiple length separated by comma, like "9,10"