Commit f68cd9c0 authored by npappas's avatar npappas

config files for all domains

parent 854f4b7d
{
"FilterDomainFastas.filterScriptPath": "/exports/sascstudent/project-RefseqRelease/src/demo_test/refseqtools/filter_fasta.py",
"FilterDomainFastas.domainInputDir": "/exports/sascstudent/project-RefseqRelease/data/release90/library/archaea",
"FilterDomainFastas.taxDbPath": "/exports/sascstudent/project-RefseqRelease/data/taxonomy/ete3_taxadb",
"FilterDomainFastas.outputDir": "/exports/sascstudent/project-RefseqRelease/analysis/complete90/library_filtered/archaea",
"FilterDomainFastas.FilterFasta.preCommand": "source activate ete3",
"FilterDomainFastas.dustmaskerExe": "/home/npappas/src/ncbi-blast-2.6.0+/bin/dustmasker",
"FilterDomainFastas.refseqJson": "/exports/sascstudent/project-RefseqRelease/analysis/demo_test/Refseq90.DNA.json",
"FilterDomainFastas.dustmaskOnly": true
}
{
"FilterDomainFastas.filterScriptPath": "/exports/sascstudent/project-RefseqRelease/src/demo_test/refseqtools/filter_fasta.py",
"FilterDomainFastas.includeAccFile": "/exports/sascstudent/project-RefseqRelease/data/accession_sets/bacteria_rep/accessions.txt",
"FilterDomainFastas.domainInputDir": "/exports/sascstudent/project-RefseqRelease/data/release90/library/bacteria",
"FilterDomainFastas.taxDbPath": "/exports/sascstudent/project-RefseqRelease/data/taxonomy/ete3_taxadb",
"FilterDomainFastas.outputDir": "/exports/sascstudent/project-RefseqRelease/analysis/complete90/library_filtered/bacteria",
"FilterDomainFastas.FilterFasta.preCommand": "source activate ete3",
"FilterDomainFastas.dustmaskerExe": "/home/npappas/src/ncbi-blast-2.6.0+/bin/dustmasker",
"FilterDomainFastas.refseqJson": "/exports/sascstudent/project-RefseqRelease/analysis/demo_test/Refseq90.DNA.json"
}
{
"FilterDomainFastas.filterScriptPath": "/exports/sascstudent/project-RefseqRelease/src/demo_test/refseqtools/filter_fasta.py",
"FilterDomainFastas.domainInputDir": "/exports/sascstudent/project-RefseqRelease/data/release90/library/fungi",
"FilterDomainFastas.taxDbPath": "/exports/sascstudent/project-RefseqRelease/data/taxonomy/ete3_taxadb",
"FilterDomainFastas.outputDir": "/exports/sascstudent/project-RefseqRelease/analysis/complete90/library_filtered/fungi",
"FilterDomainFastas.FilterFasta.preCommand": "source activate ete3",
"FilterDomainFastas.dustmaskerExe": "/home/npappas/src/ncbi-blast-2.6.0+/bin/dustmasker",
"FilterDomainFastas.refseqJson": "/exports/sascstudent/project-RefseqRelease/analysis/demo_test/Refseq90.DNA.json",
"FilterDomainFastas.dustmaskOnly": true
}
{
"FilterDomainFastas.filterScriptPath": "/exports/sascstudent/project-RefseqRelease/src/demo_test/refseqtools/filter_fasta.py",
"FilterDomainFastas.excludeAccFile": "/exports/sascstudent/project-RefseqRelease/data/accession_sets/redundant_accessions/redundant_accessions.txt",
"FilterDomainFastas.domainInputDir": "/exports/sascstudent/project-RefseqRelease/data/release90/library/invertebrate",
"FilterDomainFastas.taxDbPath": "/exports/sascstudent/project-RefseqRelease/data/taxonomy/ete3_taxadb/taxa.sqlite",
"FilterDomainFastas.outputDir": "/exports/sascstudent/project-RefseqRelease/analysis/complete90/library_filtered/invertebrate",
"FilterDomainFastas.FilterFasta.preCommand": "source activate ete3",
"FilterDomainFastas.dustmaskerExe": "/home/npappas/src/ncbi-blast-2.6.0+/bin/dustmasker",
"FilterDomainFastas.refseqJson": "/exports/sascstudent/project-RefseqRelease/analysis/demo_test/Refseq90.DNA.json"
}
{
"FilterDomainFastas.filterScriptPath": "/exports/sascstudent/project-RefseqRelease/src/demo_test/refseqtools/filter_fasta.py",
"FilterDomainFastas.excludeAccFile": "/exports/sascstudent/project-RefseqRelease/data/accession_sets/redundant_accessions/redundant_accessions.txt",
"FilterDomainFastas.domainInputDir": "/exports/sascstudent/project-RefseqRelease/data/release90/library/plant",
"FilterDomainFastas.taxDbPath": "/exports/sascstudent/project-RefseqRelease/data/taxonomy/ete3_taxadb",
"FilterDomainFastas.outputDir": "/exports/sascstudent/project-RefseqRelease/analysis/complete90/library_filtered/plant",
"FilterDomainFastas.FilterFasta.preCommand": "source activate ete3",
"FilterDomainFastas.dustmaskerExe": "/home/npappas/src/ncbi-blast-2.6.0+/bin/dustmasker",
"FilterDomainFastas.refseqJson": "/exports/sascstudent/project-RefseqRelease/analysis/demo_test/Refseq90.DNA.json"
}
{
"FilterDomainFastas.filterScriptPath": "/exports/sascstudent/project-RefseqRelease/src/demo_test/refseqtools/filter_fasta.py",
"FilterDomainFastas.domainInputDir": "/exports/sascstudent/project-RefseqRelease/data/release90/library/protozoa",
"FilterDomainFastas.taxDbPath": "/exports/sascstudent/project-RefseqRelease/data/taxonomy/ete3_taxadb",
"FilterDomainFastas.outputDir": "/exports/sascstudent/project-RefseqRelease/analysis/complete90/library_filtered/protozoa",
"FilterDomainFastas.FilterFasta.preCommand": "source activate ete3",
"FilterDomainFastas.dustmaskerExe": "/home/npappas/src/ncbi-blast-2.6.0+/bin/dustmasker",
"FilterDomainFastas.refseqJson": "/exports/sascstudent/project-RefseqRelease/analysis/demo_test/Refseq90.DNA.json",
"FilterDomainFastas.dustmaskOnly": true
}
{
"FilterDomainFastas.filterScriptPath": "/exports/sascstudent/project-RefseqRelease/src/demo_test/refseqtools/filter_fasta.py",
"FilterDomainFastas.excludeAccFile": "/exports/sascstudent/project-RefseqRelease/data/accession_sets/redundant_accessions/redundant_accessions.txt",
"FilterDomainFastas.excludeAccPrefixes": ["NR", "NG"],
"FilterDomainFastas.includeTaxa" : ["9606", "10090", "10116"],
"FilterDomainFastas.domainInputDir": "/exports/sascstudent/project-RefseqRelease/data/release90/library/vertebrate_mammalian",
"FilterDomainFastas.taxDbPath": "/exports/sascstudent/project-RefseqRelease/data/taxonomy/ete3_taxadb/taxa.sqlite",
"FilterDomainFastas.outputDir": "/exports/sascstudent/project-RefseqRelease/analysis/complete90/library_filtered/vertebrate_mamalian",
"FilterDomainFastas.FilterFasta.preCommand": "source activate ete3",
"FilterDomainFastas.dustmaskerExe": "/home/npappas/src/ncbi-blast-2.6.0+/bin/dustmasker",
"FilterDomainFastas.refseqJson": "/exports/sascstudent/project-RefseqRelease/analysis/demo_test/Refseq90.DNA.json"
}
{
"FilterDomainFastas.filterScriptPath": "/exports/sascstudent/project-RefseqRelease/src/demo_test/refseqtools/filter_fasta.py",
"FilterDomainFastas.excludeAccFile": "/exports/sascstudent/project-RefseqRelease/data/accession_sets/redundant_accessions/redundant_accessions.txt",
"FilterDomainFastas.domainInputDir": "/exports/sascstudent/project-RefseqRelease/data/release90/library/vertebrate_other",
"FilterDomainFastas.taxDbPath": "/exports/sascstudent/project-RefseqRelease/data/taxonomy/ete3_taxadb/taxa.sqlite",
"FilterDomainFastas.outputDir": "/exports/sascstudent/project-RefseqRelease/analysis/complete90/library_filtered/vertebrate_other",
"FilterDomainFastas.FilterFasta.preCommand": "source activate ete3",
"FilterDomainFastas.dustmaskerExe": "/home/npappas/src/ncbi-blast-2.6.0+/bin/dustmasker",
"FilterDomainFastas.refseqJson": "/exports/sascstudent/project-RefseqRelease/analysis/demo_test/Refseq90.DNA.json"
}
{
"FilterDomainFastas.filterScriptPath": "/exports/sascstudent/project-RefseqRelease/src/demo_test/refseqtools/filter_fasta.py",
"FilterDomainFastas.domainInputDir": "/exports/sascstudent/project-RefseqRelease/data/release90/library/viral",
"FilterDomainFastas.taxDbPath": "/exports/sascstudent/project-RefseqRelease/data/taxonomy/ete3_taxadb",
"FilterDomainFastas.outputDir": "/exports/sascstudent/project-RefseqRelease/analysis/complete90/library_filtered/viral",
"FilterDomainFastas.FilterFasta.preCommand": "source activate ete3",
"FilterDomainFastas.dustmaskerExe": "/home/npappas/src/ncbi-blast-2.6.0+/bin/dustmasker",
"FilterDomainFastas.refseqJson": "/exports/sascstudent/project-RefseqRelease/analysis/demo_test/Refseq90.DNA.json",
"FilterDomainFastas.dustmaskOnly": true
}
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