config.json

{
    "augustus": {
        "software" : "/hps/nobackup2/production/ensembl/jma/src/Augustus/bin/augustus",
        "bam2hints_path" : "/homes/fergal/bin/bam2hints",
        "bam2wig_path" : "/homes/fergal/bin/bam2wig",
        "wig2hints_path" : "/homes/fergal/bin/wig2hints"
    },
    "cmsearch": {
        "software": "cmsearch",
        "rfam_dbname" : "Rfam",
        "rfam_user" : "rfamro",
        "rfam_host" : "mysql-rfam-public.ebi.ac.uk",
        "rfam_port" : "4497",
        "rfam_cm_db_path" : "/hps/nobackup/flicek/ensembl/genebuild/blastdb/ncrna/Rfam_14.0/Rfam.cm",
        "rfam_seeds_file_path" : "/hps/nobackup/flicek/ensembl/genebuild/blastdb/ncrna/Rfam_14.0/Rfam.seed"
    },
    "convert2blastmask": {
        "software": "convert2blastmask"
    },
    "cpc2": {
        "software": "/hps/software/users/ensembl/genebuild/genebuild_virtual_user/singularity/test_cpc2.sif"
    },
    "cpg": {
        "software": "cpg_lh",
        "cpg_min_length" : "400",
        "cpg_min_gc_content" : "50",
        "cpg_min_oe" : "0.6"
    },
    "dust": {
        "software": "dustmasker"
    },
    "eponine": {
        "software": "/hps/software/users/ensembl/ensw/C8-MAR21-sandybridge/linuxbrew/opt/eponine/libexec/eponine-scan.jar",
        "threshold" : "0.999"
    },
    "genblast": {
        "software": "genblast"
    },
    "java": {
        "path": "java"
    },
    "makeblastdb" : {
        "software" : "makeblastdb"
    },
    "minimap2" : {
        "software" : "minimap2",
        "paftools_path" : "paftools.js"
    },
    "red": {
        "software": "Red"
    },
    "rnasamba": {
        "software": "/hps/software/users/ensembl/genebuild/genebuild_virtual_user/singularity/rnasamba_latest.sif",
        "weights" : "/nfs/production/flicek/ensembl/genebuild/genebuild_virtual_user/rnasamba_data/full_length_weights.hdf5"
    },
    "repeatmasker": {
        "software": "RepeatMasker",
        "engine" : "rmblast"
    },
    "star": {
        "software": "STAR"
    },
    "trf": {
        "software": "trf",
        "match_score": 2,
        "mismatch_score" : 5,
        "delta" : 7,
        "pm" : 80,
        "pi" : 10,
        "minscore" : 40,
        "maxperiod" : 500
    },
    "trnascan": {
        "software": "/hps/software/users/ensembl/ensw/C8-MAR21-sandybridge/linuxbrew/bin/tRNAscan-SE",
        "filter_path" : "/hps/software/users/ensembl/ensw/C8-MAR21-sandybridge/linuxbrew/bin/EukHighConfidenceFilter"
    }
}