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# deconstructSigs signatures.cosmic
library("deconstructSigs")
library("tibble")
signatures.cosmic.tidy <- tibble::rownames_to_column(as.data.frame(t(signatures.cosmic)))

# COSMIC http://cancer.sanger.ac.uk/cancergenome/assets/signatures_probabilities.txt
cosmic.current <- read.delim("http://cancer.sanger.ac.uk/cancergenome/assets/signatures_probabilities.txt", check.names = F)
cosmic.current.clean <- cosmic.current[ , colnames(cosmic.current) != ""]
cosmic.current.tidy <- cosmic.current.clean[,names(cosmic.current.clean) not in c("Substitution Type","Trinucleotide")]

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FROM ubuntu:17.10

ENV LANG C.UTF-8

RUN apt-get update && \
    apt-get install -y python3 python3-pip libxml2-dev zlib1g-dev wget git cmake && \
    apt-get clean

RUN apt-get install -y python3-numpy # not necessary in scanpy 0.2.9.2/0.2.10

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# relation-data
ddr:
  evidence-count: 3
  score-threshold: 0.1

# association-data
scoring_weights:
  crisp: 1
  europepmc: 0.2
  expression_atlas: 0.2

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# [invalid-]evidence-data
evidences:
  gs_output_dir: evidence-files
  downloads:
  - bucket: otar000-evidence_input/CRISPR/json
    output_filename: crispr-{suffix}.json.gz
    resource: input-file
    subset_key:
    - target
    - id