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monarch-initiative / exomiser-phenotype-data-revised

Repo for generating monarch data dependencies like the one used by exomiser
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Fix old data dependencies #1

Open matentzn opened 5 years ago

matentzn commented 5 years ago

Currently the phenodigm score generation relies on some old datasets located in monarch-initiative/monarch-owlsim-data.

@kshefchek What should these be replaced with:

# OWLSIM DATA
MONARCH_OWLSIM_DATA=https://raw.githubusercontent.com/monarch-initiative/monarch-owlsim-data/master/data
URL_MP_G2P=$(MONARCH_OWLSIM_DATA)/Mus_musculus/Mm_gene_phenotype.txt
URL_MP_GL=$(MONARCH_OWLSIM_DATA)/Mus_musculus/Mm_gene_labels.txt
URL_HP_D2P=$(MONARCH_OWLSIM_DATA)/Homo_sapiens/Hs_disease_phenotype.txt
URL_HP_DL=$(MONARCH_OWLSIM_DATA)/Homo_sapiens/Hs_disease_labels.txt
URL_ZP_G2P=$(MONARCH_OWLSIM_DATA)/Danio_rerio/Dr_gene_phenotype.txt
URL_ZP_GL=$(MONARCH_OWLSIM_DATA)/Danio_rerio/Dr_gene_labels.txt
kshefchek commented 5 years ago

Currently these are generated on the fly using our development database, but I would like to make these files part of our release, so they would end up in https://archive.monarchinitiative.org/latest/

https://github.com/monarch-initiative/jenkins/blob/master/Jenkinsfile#L368

matentzn commented 5 years ago

Perfect! Thanks for letting me know. I dont want to add yet another variables in this enormous process yet; so I will poke you again when I want to move to the next level. Thanks.