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lines changedSubmodule g2p-aggregator updated 35 files
- data/.gitignore+20
- data/Makefile+55-15
- data/clinvar/get_clinvar_latest.sh+32
- data/cosmic_to_sqlite.sh+64
- data/genesets/cosmic/Census_allMon Jan 20 12_34_38 2020.tsv+724
- data/genesets/cosmic/cancer_gene_census.csv+724
- data/genesets/merged/.gitignore+1
- data/genesets/merged/acquire_merged_list.sh+45
- data/get_cosmic_creds.sh+21
- data/get_cosmic_datafile.sh+28
- data/get_oncokb_creds.sh+20
- harvester/Dockerfile+1-1
- harvester/entrypoint.sh+43-6
- harvester/entrypoint_debug.sh-29
- harvester/harvester.py+108-92
- harvester/harvesters/clinvar.py+39-16
- harvester/harvesters/cosmic.py+144-172
- harvester/normalizers/gene_enricher.py+1-1
- harvester/phases/__init__.py+2
- harvester/phases/vep_annotate.py+5
- harvester/postprocess/vep/annotate_variants.py+40
- harvester/postprocess/vep/exec_vep.sh+19
- harvester/postprocess/vep/image/Dockerfile+17
- harvester/postprocess/vep/image/ensure_cache.sh+3
- harvester/postprocess/vep/image/entrypoint.sh+13
- harvester/postprocess/vep/input_variants.txt+10
- harvester/silos/postgres_silo.py+81-68
- harvester/utils_ex/downloading.py+30-21
- notebooks/clinvar/variation_archive.xsd+2.3k
- notebooks/clinvar_support.py
- notebooks/format_tools.py+33
- notebooks/launch_nb.sh+5
- notebooks/parse_clinvar.ipynb+12.3k
- notebooks/ui_tests.ipynb+21.8k
- notebooks/xml_tree.py+48
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