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defaults_nesi.cfg
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/
defaults_nesi.cfg
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#
# Defaults config file for VCF process
#
# If the executables are on your path
# just the executable name is required.
#
# ? is the willcard flag for the prefix options
[system]
cores_avaliable = 10
# Library settings do not change, the library folder are appended to the path when runnig the program#
[environment]
LD_LIBRARY_PATH=/home/murray.cadzow/uoo00008/MerrimanSelectionPipeline/lib
PERL5LIB=/home/murray.cadzow/uoo00008/MerrimanSelectionPipeline/lib/perl5
[selection_pipeline]
selection_pipeline_executable = ~/.local/bin/selection_pipeline
[vcftools]
vcf_tools_executable = /home/murray.cadzow/uoo00008/MerrimanSelectionPipeline/bin/vcftools
vcf_subset_executable = /home/murray.cadzow/uoo00008/MerrimanSelectionPipeline/bin/vcf-subset
vcf_merge_executable = /home/murray.cadzow/uoo00008/MerrimanSelectionPipeline/bin/vcf-merge
vcf_concat_executable = /home/murray.cadzow/uoo00008/MerrimanSelectionPipeline/bin/vcf-concat
extra_args=
[genetic_map]
genetic_map_dir= /home/murray.cadzow/uoo00008/MerrimanSelectionPipeline/referencefiles/genetic_maps
genetic_map_prefix=genetic_map_chr?_combined_b37.txt
[shapeit]
shapeit_executable= /home/murray.cadzow/uoo00008/MerrimanSelectionPipeline/bin/shapeit
extra_args =
[impute2]
impute_executable = /home/murray.cadzow/uoo00008/MerrimanSelectionPipeline/bin/impute2
impute_map_dir= /home/murray.cadzow/uoo00008/MerrimanSelectionPipeline/referencefiles/impute_ref
impute_reference_dir= /home/murray.cadzow/uoo00008/MerrimanSelectionPipeline/referencefiles/impute_ref/ALL_1000G_phase1integrated_v3_impute
impute_map_prefix=genetic_map_chr?_combined_b37.txt
impute_reference_prefix=ALL_1000G_phase1integrated_v3_chr?_impute
extra_args =
[plink]
plink_executable =/home/murray.cadzow/uoo00008/MerrimanSelectionPipeline/bin/plink
extra_args =
[Rscript]
rscript_executable = Rscript
indel_filter = /home/murray.cadzow/uoo00008/MerrimanSelectionPipeline/corescripts/haps_indel_and_maf_filter.R
generate_rsb = /home/murray.cadzow/uoo00008/MerrimanSelectionPipeline/corescripts/generate_rsb.R
extra_args=
[haps_scripts]
haps_to_hapmap_script= /home/murray.cadzow/.local/bin/haps_to_hapmap
haps_filter_script = /home/murray.cadzow/.local/bin/haps_filters
haps_interpolate_script = /home/murray.cadzow/.local/bin/haps_interpolate
[ancestral_allele]
split_by_chromosome = True
# not used unless split_by_chromosome is set to False
ancestral_fasta_header_regex =
# not used unless split_by_chromosome is set to False
ancestral_fasta_file =
ancestral_allele_script= /home/murray.cadzow/.local/bin/ancestral_annotation
ancestral_fasta_dir=/home/murray.cadzow/uoo00008/MerrimanSelectionPipeline/referencefiles/ancestral_ref
ancestral_prefix=human_ancestor_?.fa
[qctool]
qctool_executable=/home/murray.cadzow/uoo00008/MerrimanSelectionPipeline/bin/qctool
[multicore_ihh]
multicore_ihh = /home/murray.cadzow/uoo00008/MerrimanSelectionPipeline/corescripts/multicore_iHH.R
[variscan]
variscan_executable = /home/murray.cadzow/uoo00008/MerrimanSelectionPipeline/bin/variscan
[java]
java_executable = /usr/bin/java
[beagle]
beagle_jar = /home/murray.cadzow/uoo00008/MerrimanSelectionPipeline/bin/beagle.jar
vm_size = 4g