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cfg_file_shigella.yml
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cfg_file_shigella.yml
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---
A_General:
dir_files: '/biologia-scratch3/l.perlaza149/DeEP_Pro/Shigella_genomes'
dir_out: '/biologia-scratch3/l.perlaza149/DeEP_Pro/Shigella_genomes_output'
job_name: Shigella_paper
names: Shigella_sonnei_53G.fasta,Escherichia_coli_SE11.fasta,Shigella_flexneri_2a_str_301.fasta,Shigella_boydii_CDC_3083-94.fasta,Escherichia_coli_ETEC_H10407.fasta,Shigella_dysenteriae_Sd197.fasta,Escherichia_coli_K-12_MG1655.fasta,Shigella_sonnei_Ss046.fasta,Shigella_boydii_Sb227.fasta,Shigella_flexneri_2002017.fasta,Shigella_dysenteriae_1617.fasta
num_genomes: Shigella_sonnei_53G.fasta,Escherichia_coli_SE11.fasta,Shigella_flexneri_2a_str_301.fasta,Shigella_boydii_CDC_3083-94.fasta,Escherichia_coli_ETEC_H10407.fasta,Shigella_dysenteriae_Sd197.fasta,Escherichia_coli_K-12_MG1655.fasta,Shigella_sonnei_Ss046.fasta,Shigella_boydii_Sb227.fasta,Shigella_flexneri_2002017.fasta,Shigella_dysenteriae_1617.fasta
num_regions: ~
B_MAUVE:
path_mauve: '/datos-biologia/BioProgs/gainloss/MAUVE/'
C_MAUVE_output:
backbone: '/biologia-scratch3/l.perlaza149/DeEP_Pro/Shigella_genomes_output/Shigella.backbone'
tree: '/biologia-scratch3/l.perlaza149/DeEP_Pro/Shigella_genomes_output/Shigella.tree'
xmfa: '/biologia-scratch3/l.perlaza149/DeEP_Pro/Shigella_genomes_output/Shigella.xmfa'
D_ssLCBs:
length: 500
path_ssLCBs: '/datos-biologia/BioProgs/gainloss/MAUVE/utility/'
E_ssLCBs_output:
bbcols: '/biologia-scratch3/l.perlaza149/DeEP_Pro/Shigella_genomes_output/Shigella.xmfa.bbcols'
core: '/biologia-scratch3/l.perlaza149/DeEP_Pro/Shigella_genomes_output/Shigella.core_alignment.xmfa'
F_Blocksplit:
num_blocks: 809
path_blocksplit: '/datos-biologia/BioProgs/gainloss/clonalorigin/warg/scripts/'
G_Result:
Binary_File: '/biologia-scratch3/l.perlaza149/DeEP_Pro/Shigella_genomes_output/Shigella.backbone.binary'
Summary_File: '/biologia-scratch3/l.perlaza149/DeEP_Pro/Shigella_output/Shigella.Rcomb_4.00e-01.out'
H_ClonalFrame:
burn_in: 10000
interval: 100
iterations: 10000
others: ' -v '
parallel: 10
path_ClonalFrame: '/datos-biologia//BioProgs/gainloss/ClonalFrame/bin/'
threshold: 5.00e-01
I_ClonalFrame_output:
clonal_concensus: '/biologia-scratch3/l.perlaza149/DeEP_Pro/Shigella_genomes_output/Shigella.clonalframe.out.1'
J_ClonalTree:
path_clonaltree: '/datos-biologia/BioProgs/gainloss/clonalorigin/warg/scripts/'
K_ClonalTree_output:
final_tree: ''
L_Result:
Binary_file: ''
Summary_File: '/biologia-scratch3/l.perlaza149/DeEP_Pro/Shigella_genomes_output/Shigella.Rcomb_5.00e-01.out'
M_window_acgt:
path_window: '/datos-biologia/BioProgs_SGE/glimmer3.02/bin/'
window_skip: 80
N_Rscript:
Rscript_path: '/biologia-scratch3/l.perlaza149/DeEP_Pro/DeEP_Scripts/R-3.1.1/bin/Rscript'
parallel: 10
O_Results:
Binary_file: '//data/DeEP/Genom130_Output//gc_result_pvalue.txt'
P_Patterns:
file_binary: '//data/DeEP/Genom130_Output//XAM_130.backbone.binary'
file_pattern: '//data/DeEP/Genom130_Output//XAM_130.backbone_.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,_.matrix'
pattern: '.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,'
region_name: ~
Q_AutoBLAST:
blast_task: ~
dbtype: ~
output_format: ~
path_bin: '/datos-biologia/BioProgs_SGE//ncbi-blast-2.2.25+/bin'
path_queries: ~
reference_genomes: ~