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Comment/format the rules that download remote resources.
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Group the rules that download the HRA subset and the CellxGene subset
into a new "EXTERNAL RESOURCES" section and add appropriate comments.
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gouttegd committed Oct 14, 2024
1 parent 572f609 commit 2b1f171
Showing 1 changed file with 12 additions and 3 deletions.
15 changes: 12 additions & 3 deletions src/ontology/cl.Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -305,17 +305,26 @@ add-replacedby:
convert -f ofn -o $(SRC)


## Download human reference atlas subset
# ----------------------------------------
# EXTERNAL RESOURCES
# ----------------------------------------

# Human reference atlas subset
# FIXME: Refreshing of this resource should be uncoupled from the
# release/QC pipelines.
# See <https://github.com/obophenotype/cell-ontology/issues/2644>
HRA_SUBSET_URL="https://raw.githubusercontent.com/hubmapconsortium/ccf-validation-tools/master/owl/CL_ASCTB_subset.owl"
$(TMPDIR)/hra_subset.owl:
wget $(HRA_SUBSET_URL) -O $@

$(COMPONENTSDIR)/hra_subset.owl: $(TMPDIR)/hra_subset.owl
$(ROBOT) merge -i $< annotate --ontology-iri $(ONTBASE)/$@ --output $@

## Download CellXGene reference subset

# CellXGene reference subset
# FIXME: Never actually downloaded again, unless the
# $(TEMPLATEDIR)/cellxgene_subset.tsv file is manually removed; probably
# not what was intended.
# See <https://github.com/obophenotype/cell-ontology/issues/2644>
CELLXGENE_SUBSET_URL="https://raw.githubusercontent.com/hkir-dev/cellxgene-cell-reporter/main/templates/cellxgene_subset.tsv"
$(TEMPLATEDIR)/cellxgene_subset.tsv:
wget $(CELLXGENE_SUBSET_URL) -O $@
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