config.ini

## This configuration file points to programs and reference files used by MuPeXI.
## The file is structured so groups are stated in [] and names underneath folowed by =.
## You should ONLY change the path to your references, not the groups nor the names. 

[netMHC]
# Please specify the NetMHCpan binary path
MHC = /your/path/to/netmhcpan/4.0a/netMHCpan

[EnsemblVEP]
# Please specify path to the Ensembl Variant effect predictor (VEP) binary, and the 
# directory containing the cache database. 
# The VEPdir is the directory containing the cached references. (human/GRCh38)
VEP = /your/path/to/ensembl-vep/release-95.1/vep
VEPdir = /your/path/to/databases/variant_effect_predictor/.vep

[References]
# Please specify the path to the reference files 
# NOTE: The individual peptide reference files (pep8 etc.) are generated by MuPeXI in the
# first run, and can be obtained and saved by keeping temporary files (-t option)  
cDNA = /your/path/to/human_GRCh38/cDNA/Homo_sapiens.GRCh38.95.cdna.all.fa
pep = /your/path/to/human_GRCh38/pep/Homo_sapiens.GRCh38.95.pep.all.fa
cosmic = /your/path/to/human_GRCh38/cosmic/Census_allWed_Feb_17_09-33-40_2016.tsv
#pep8 = /your/path/to/references/reference_peptide_8.txt
#pep9 = /your/path/to/references/reference_peptide_9.txt
#pep10 = /your/path/to/references/reference_peptide_10.txt
#pep11 = /your/path/to/references/reference_peptide_11.txt

[PeptideMatch]
# Please specify the path to the pepmatch binary file matching your operating system
PM = /your/path/to/MuPeXI/bin/pepmatch_db_x86_64

[LiftOver]
# Optional, only necessary when using the GRCh37 genome reference
#fasta = /your/path/to/references/human_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fa
#chain = /your/path/to/references/human_GRCh37/liftover/hg19ToHg38.over.chain
#java8 = /your/path/to/java/jre1.8.0_102/bin/java
#picard = /your/path/to/picard-tools-2.5.0