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loc_sanger.config
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loc_sanger.config
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env {
PATH = "${ROOTDIR}/RATT:${ROOTDIR}/ABACAS2:${HOME}/annot/software/ORTHOMCLV1.4:${HOME}/genometools/bin:/software/pathogen/external/apps/usr/local/tmhmm-2.0c/bin:${HOME}/annot/software/augustus-3.0.3/bin:/software/pathogen/external/apps/usr/bin:$PATH"
RATT_HOME = "${ROOTDIR}/RATT"
RATT_CONFIG = "${ROOTDIR}/RATT/RATT.config_euk_NoPseudo_SpliceSite"
GT_RETAINIDS = "yes"
PFAM = "/lustre/scratch108/parasites/ss34/pfam/Pfam-A.hmm"
SNAP_MODEL = "${ROOTDIR}/data/snap/LmjF.hmm"
AUGUSTUS_CONFIG_PATH = "${ROOTDIR}/data/augustus"
FILTER_SHORT_PARTIALS_RULE = "${ROOTDIR}/data/filters/filter_short_partials.lua"
PFAM2GO = "${ROOTDIR}/data/pfam2go/pfam2go.txt"
}
params.GO_OBO = "${HOME}/go.obo"
params.NCRNA_MODELS = "${ROOTDIR}/data/cm/kinetoplastid_rnas.cm"
params.CIRCOS_CONFIG_FILE = "${ROOTDIR}/data/circos/circos.conf"
params.CIRCOS_BIN_CONFIG_FILE = "${ROOTDIR}/data/circos/circos.bin.conf"
params.SPECFILE = "${ROOTDIR}/data/speck/new_gff_format.lua"
params.AUGUSTUS_EXTRINSIC_CFG = "${ROOTDIR}/data/augustus/extrinsic.cfg"
executor {
name = 'local'
queueSize = 10
pollInterval = '3sec'
}