new release

Makefile

@@ -1,6 +1,8 @@
 # TODO: parse from yaml
-BUILDS = hg38 ce11 mm10 rn6 galGal6
+# https://hgdownload.soe.ucsc.edu/downloads.html
+BUILDS = hg38 ce11 mm39 rn6 galGal6 calJac4 danRer11
 # TODO: dm6
+RUN = poetry run
 
 all: all-chromAlias all-cytoBand src/ontology/components/ucsc.owl  all-components ontology
 all-chromAlias: $(patsubst %, download/%-chromAlias.tsv, $(BUILDS))
@@ -18,29 +20,32 @@ test:
 	pytest
 
 download/%-chromAlias.tsv:
-	curl -L -s http://hgdownload.cse.ucsc.edu/goldenPath/$*/database/chromAlias.txt.gz | gzip -dc > $@
+	curl -L -s http://hgdownload.cse.ucsc.edu/goldenPath/$*/database/chromAlias.txt.gz | gzip -dc > $@.tmp && mv $@.tmp $@
 download/%-cytoBand.tsv:
-	curl -L -s http://hgdownload.cse.ucsc.edu/goldenPath/$*/database/cytoBand.txt.gz | gzip -dc > $@
+	curl -L -s http://hgdownload.cse.ucsc.edu/goldenPath/$*/database/cytoBandIdeo.txt.gz | gzip -dc > $@.tmp && mv $@.tmp $@
+#	curl -L -s http://hgdownload.cse.ucsc.edu/goldenPath/$*/database/cytoBand.txt.gz | gzip -dc > [email protected] && mv [email protected] $@
 download/ce11-cytoBand.tsv:
-	curl -L -s http://hgdownload.cse.ucsc.edu/goldenPath/ce11/database/cytoBandIdeo.txt.gz | gzip -dc > $@
+	curl -L -s http://hgdownload.cse.ucsc.edu/goldenPath/ce11/database/cytoBandIdeo.txt.gz | gzip -dc > $@.tmp && mv $@.tmp $@
 download/danRer10-cytoBand.tsv:
-	curl -L -s http://hgdownload.cse.ucsc.edu/goldenPath/danRer10/database/cytoBandIdeo.txt.gz | gzip -dc > $@
+	curl -L -s http://hgdownload.cse.ucsc.edu/goldenPath/danRer10/database/cytoBandIdeo.txt.gz | gzip -dc > $@.tmp && mv $@.tmp $@
 download/galGal6-cytoBand.tsv:
-	curl -L -s http://hgdownload.cse.ucsc.edu/goldenPath/galGal6/database/cytoBandIdeo.txt.gz | gzip -dc > $@
+	curl -L -s http://hgdownload.cse.ucsc.edu/goldenPath/galGal6/database/cytoBandIdeo.txt.gz | gzip -dc > $@.tmp && mv $@.tmp $@
+download/calJac4-cytoBand.tsv:
+	curl -L -s http://hgdownload.cse.ucsc.edu/goldenPath/calJac4/database/cytoBandIdeo.txt.gz | gzip -dc > $@.tmp && mv $@.tmp $@
 components/%.owl: download/%-cytoBand.tsv download/%-chromAlias.tsv
-	python -m monochrom.monochrom $^ -o $@
+	$(RUN) ucsc2owl $^ -o $@
 components/%.yaml: download/%-cytoBand.tsv download/%-chromAlias.tsv
-	python -m monochrom.monochrom $^ -f yaml -o $@
+	$(RUN) ucsc2owl $^ -f yaml -o $@
 
 download/ncit.owl:
-	curl -L -s http://purl.obolibrary.org/obo/ncit.owl > $@
+	curl -L -s http://purl.obolibrary.org/obo/ncit.owl > $@.tmp && mv $@.tmp $@
 
 download/ncit-chrom-terms.owl: download/ncit.owl config/ncit-chrom-terms.txt
 	robot extract -i $< -m TOP -T config/ncit-chrom-terms.txt -o $@
 
 # ODK will take things on from here
 src/ontology/tmp/ucsc.ofn: monochrom/monochrom.py monochrom/chromschema.py
-	python -m monochrom.monochrom download/*-*.tsv -o $@.tmp && mv $@.tmp $@
+	$(RUN) ucsc2owl download/*-*.tsv -o $@.tmp && mv $@.tmp $@
 .PRECIOUS: src/ontology/tmp/ucsc.ofn
 
 ONTBASE=http://purl.obolibrary.org/obo/chr
@@ -51,7 +56,7 @@ src/ontology/components/ucsc.owl: src/ontology/tmp/ucsc.ofn
 ## Schema
 
 monochrom/chromschema.py: model/schema/chromo.yaml
-	gen-py-classes model/schema/chromo.yaml > $@
+	gen-pydantic model/schema/chromo.yaml > $@.tmp && mv $@.tmp $@
 
 gendocs:
 	gen-markdown -d docs model/schema/chromo.yaml

README.md

@@ -86,7 +86,7 @@ http://purl.obolibrary.org/obo/chr.owl  (once this ontology is registered)
 From the top level of this repo:
 
 ```bash
-pip install -r requirements.txt
+poetry install
 make
 ```
 
@@ -99,7 +99,7 @@ make prepare_release
 
 The [Makefile](Makefile) and the metadata file [genomes.yaml](genomes.yaml) drive the python code in [monochrom/](monochrom/).
 
-To add more genomes, it is necessary to etxend both the Makefile and the genomes metadata file, but this could be made more elegant in the future.
+To add more genomes, it is necessary to extend both the Makefile and the genomes metadata file, but this could be made more elegant in the future.
 
 If you wish to modify the code, here is how it is structured, and the underlying philosophy.