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kundajelab / bpnet

Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
http://bit.ly/bpnet-colab
MIT License
141 stars 33 forks source link

examples file snakefile #27

Closed liameihao closed 3 years ago

liameihao commented 3 years ago

rule chip_seq: input: [os.path.normpath(os.path.join('data', f)) for f in DataSpec.load('chip-nexus/dataspec.yml').list_all_files(include_peaks=True)]

should be: for f in DataSpec.load('chip-seq/dataspec.yml').list_all_files(include_peaks=True)]

liameihao commented 3 years ago

and chip-seq can not download,

may add:

rule download_fasta_1: """Download an individual file """ output: f = 'data/mm10_no_alt_analysis_set_ENCODE.fasta' params: base_url = base_url shell: "wget {params.base_url}/mm10_no_alt_analysis_set_ENCODE.fasta -O {output.f}"