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context.config
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context.config
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#################################
## General Info ##
#################################
## The project name. Folders and output files will contain this name
project_name=
## Email. Only needed if MSI mode is 'true'
input_email=
## Full physical path to the reference genome
referenceGenome=
## The location of the .VCF input file
input_file=
## The output location. If not specified, the output directory will be saved to the input location
output_location=
## Single Nucleotide Deletion - SND mode
## 1 = SND mode on
## 2 = SND mode off
sndMode=1
#################################
## MSI Options ##
#################################
## MSI mode, set this to true if you are on the University of Minnesota's Supercomputer. Otherwise, set to false.
MSI_Mode=true
## If MSI mode is true, then fill out the these parameters
## The cluster resources needed to complete the job. Check out (https://www.msi.umn.edu/queues) for parameters.
job_specs="mem=40gb,nodes=1:ppn=16,walltime=24:00:00"
## Choose what MSI cluster you would like to run your job on
queue=mesabi
#################################
## Mutation Motif ##
#################################
## How large would you like to expand the coverage window in bp (min 1, max 99)
window_length=0
## The mutation motif flanks around the original nucleotide in bp (min 0, max 2)
flanks=0
## The minimum allowable percent of indels in your FASTA files (min 25, max 100)
indel_max_amount=25
#################################
## Mutation Analysis ##
#################################
## Would you like to generate motif graphs (true or false)
mutation_analysis=true
## Would you like to generate graphs for each direction
## 1 = generate graphs for each direction tables and combined counts table
## 2 = generate graphs for each direction tables ONLY
## 3 = generate graph for combine counts table ONLY
graphs=1
## Would you like to use nbr or spectra argument - defaults to nbr
## 1 = nbr
## 2 = spectra
nbr_or_spectra=1
## Would you like to use strand-symmetry or None - defaults to strand-symmetry
## 1 = strand symmetry
## 2 = none
strand_symmetry_or_asymmetry=1
#################################
## Saving Options ##
#################################
## All intermediate files are saved (parsed VCF, BED files, FASTA files)
save_all_data=false
## Save output directory to Amazon S3 storage, for non-MSI S3 - make sure you have your 'aws' credentials in your home directory.
## Follow these instructions below for non-MSI users, or msi users who want to use their own personal S3 accounts:
## https://docs.aws.amazon.com/config/latest/developerguide/gs-cli.htmll
## Choose 0 - 3:
## 0: No S3
## 1: MSI S3 only
## 2: External Amazon S3 ONLY (Needs .aws in home dir)
## 3: Save on BOTH MSI S3 and Amazon's external S3
save_S3=0
## Save counts tables to your Dropbox app (https://www.dropbox.com/developers/apps)
dropbox=false
## Your Dropbox auth code, leave blank if you're not using
dropbox_auth=
## GitHub
github=false
## GitHub username and password, leave blank if you're not using
## These will be redacted from config file when uploaded to GitHub
gitUser=
gitPass=
## The repository (repo) name you will be up loading to, leave blank if you're not using
Myrepository=
## The repo's owner (their username), if it's your repo you just leave empty, leave blank if you're not using
owner=