Make cleaning

2025-11-16 14:56:03 +01:00
parent 35d275c104
commit 30b7175702
367 changed files with 170866 additions and 11173 deletions
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/Makefile
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/Makefile
@@ -0,0 +1,103 @@
+SHELL := /bin/bash
+FTPNCBI=ftp.ncbi.nlm.nih.gov
+GBURL=https://$(FTPNCBI)/genbank
+GBRELEASE_URL=$(GBURL)/GB_Release_Number
+
+TAXOURL=https://$(FTPNCBI)/pub/taxonomy/taxdump.tar.gz
+
+GBRELEASE:=$(shell curl $(GBRELEASE_URL))
+
+GBDIV_ALL:=$(shell curl -L ${GBURL} \
+                  | grep -E 'gb.+\.seq\.gz' \
+				  | sed -E 's@^.*<a href="gb([^0-9]+)[0-9]+\.seq.gz.*$$@\1@' \
+				  | sort \
+				  | uniq)
+
+GBDIV=bct inv mam phg pln pri rod vrl vrt
+DIRECTORIES=fasta fasta_fgs
+
+GBFILE_ALL:=$(shell curl -L ${GBURL} \
+					| grep -E "gb($$(tr ' ' '|' <<< "${GBDIV}"))[0-9]+" \
+					| sed -E 's@^<a href="(gb.+.seq.gz)">.*$$@\1@')
+
+
+SUFFIXES += .d
+NODEPS:=clean taxonomy
+DEPFILES:=$(wildcard Release_$(GBRELEASE)/depends/*.d)
+
+ifeq (0, $(words $(findstring $(MAKECMDGOALS), $(NODEPS))))
+    #Chances are, these files don't exist.  GMake will create them and
+    #clean up automatically afterwards
+    -include $(DEPFILES)
+endif
+
+
+all: depends directories FORCE
+	@make downloads
+
+downloads: taxonomy fasta_files 
+	@echo Genbank Release number $(GBRELEASE)
+	@echo all divisions : $(GBDIV_ALL)
+
+FORCE:
+	@sleep 1
+
+.PHONY: all directories depends taxonomy fasta_files FORCE
+
+depends: directories Release_$(GBRELEASE)/depends/gbfiles.d Makefile
+
+division: $(GBDIV)
+
+taxonomy: directories Release_$(GBRELEASE)/taxonomy
+
+directories: Release_$(GBRELEASE)/fasta Release_$(GBRELEASE)/stamp Release_$(GBRELEASE)/tmp 
+
+Release_$(GBRELEASE):
+	@mkdir -p $@ 
+	@echo Create $@ directory
+
+Release_$(GBRELEASE)/fasta: Release_$(GBRELEASE)
+	@mkdir -p $@ 
+	@echo Create $@ directory
+
+Release_$(GBRELEASE)/stamp: Release_$(GBRELEASE)
+	@mkdir -p $@ 
+	@echo Create $@ directory
+
+Release_$(GBRELEASE)/tmp: Release_$(GBRELEASE)
+	@mkdir -p $@ 
+	@echo Create $@ directory
+
+Release_$(GBRELEASE)/depends/gbfiles.d: Makefile
+	@echo Create depends directory
+	@mkdir -p Release_$(GBRELEASE)/depends
+	@for f in ${GBFILE_ALL} ; do \
+	            echo -e "Release_$(GBRELEASE)/stamp/$$f.stamp:" ; \
+				echo -e "\t@echo Downloading file : $$f..." ; \
+				echo -e "\t@mkdir -p Release_$(GBRELEASE)/tmp" ; \
+				echo -e "\t@mkdir -p Release_$(GBRELEASE)/stamp" ; \
+				echo -e "\t@curl -L ${GBURL}/$$f > Release_$(GBRELEASE)/tmp/$$f && touch \$$@"  ; \
+				echo ; \
+				div=$$(sed -E 's@^gb(...).*$$@\1@' <<< $$f) ; \
+				fasta="Release_$(GBRELEASE)/fasta/$$div/$${f/.seq.gz/.fasta.gz}" ; \
+				fasta_fgs="Release_$(GBRELEASE)/fasta_fgs/$$div/$${f/.seq.gz/.fasta.gz}" ; \
+				fasta_files="$$fasta_files $$fasta" ; \
+				fasta_fgs_files="$$fasta_fgs_files $$fasta_fgs" ; \
+				echo -e "$$fasta: Release_$(GBRELEASE)/stamp/$$f.stamp" ; \
+				echo -e "\t@echo converting file : \$$< in fasta" ; \
+				echo -e "\t@mkdir -p Release_$(GBRELEASE)/fasta/$$div" ; \
+				echo -e "\t@obiconvert -Z --fasta-output --skip-empty  \\" ; \
+				echo -e "\t            Release_$(GBRELEASE)/tmp/$$f > Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \\" ; \
+				echo -e "\t            && mv Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \$$@  \\" ; \
+				echo -e "\t            && rm -f Release_$(GBRELEASE)/tmp/$$f  \\" ; \
+				echo -e "\t            || rm -f \$$@" ; \
+				echo -e "\t@echo conversion of $$@ done." ; \
+				echo ; \
+				done > $@ ; \
+				echo >> $@ ; \
+				echo "fasta_files: $$fasta_files" >> $@ ; 
+
+Release_$(GBRELEASE)/taxonomy: 
+	mkdir -p $@
+	curl -iL $(TAXOURL) \
+	| tar -C $@ -zxf -