include config.mk include paths.mk include ${SRC_GATHERING_PATH}/Makefile .PHONY: help docker-build docker-bash .PHONY: cleaning-manual gathering-full gathering-quick gathering-full-hard .PHONY: gathering-databases-full gathering-databases-full-hard gathering-databases-quick .PHONY: gathering-databases gathering-databases-download gathering-databases-download-modified .PHONY: gathering-databases-scrape gathering-databases-accessible gathering-databases-semi gathering-databases-closed .PHONY: gathering-custom-dictionaries gathering-pmcid gathering-gbif gathering-chinese-board gathering-validation .PHONY: gathering-translation-tcmid gathering-translation-full gathering-translation-common gathering-translation-common-quick gathering-translation-quick gathering-translation-tcm gathering-translation-tcm-quick .PHONY: gathering-taxonomy-otl gathering-taxonomy-npclassifier gathering-taxonomy-classyfire gathering-taxonomy-full .PHONY: gathering-custom-dictionaries gathering-validation .PHONY: curating curating-1-integrating curating-editing curating-3-integrating .PHONY: curating-editing-structure curating-editing-structure-translating curating-editing-structure-translating-name curating-editing-structure-translating-inchi curating-editing-structure-integrating curating-editing-structure-sanitizing curating-editing-structure-naming curating-editing-structure-classifying .PHONY: curating-editing-organism curating-editing-organism-processing-original curating-editing-organism-translating curating-editing-organism-processing-translated curating-editing-organism-processing-taxonomy .PHONY: curating-editing-reference curating-editing-reference-translating curating-editing-reference-translating-doi curating-editing-reference-translating-pubmed curating-editing-reference-translating-title curating-editing-reference-translating-split curating-editing-reference-translating-publishingDetails curating-editing-reference-translating-original curating-editing-reference-integrating curating-editing-reference-processing .PHONY: curating-and-analyzing analyzing analyzing-sampling analyzing-validating analyzing-metrics analyzing-examples .PHONY: processing-organism-interim .PHONY: curating-and-analyzing-and-visualizing visualizing visualizing-alluvial visualizing-chord visualizing-tree visualizing-upset visualizing-distribution .PHONY: get-gnfinder get-gnverifier get-opsin get-bins .PHONY: lotus-bloom lotus-check lotus-roots lotus-seeds .PRECIOUS: %.tsv %.zip %.json %.gz help: @echo "Builder" @echo "-------" @echo "" @echo "docker-build: build the docker image (with no data)" @echo "docker-bash: run a shell into the docker image" @echo "databases: build the databases (no scraping)" @echo "databases-rescrape: rescrape the databases (when possible)" @echo "" @echo "get-bins: download gnfinder, gnverify and opsin" @echo "" @echo "gathering-full: Run the 1_gathering scripts" @echo "curating: Run the 2_curating scripts" @echo "analyzing: Run the 3_analyzing scripts" @echo "visualizing: Run the 4_visualizing scripts" docker-build: docker build -t onpdb-environment --build-arg USER_ID=$(shell id -u) --build-arg GROUP_ID=$(shell id -g) . docker-bash: docker run -it --rm -v $$PWD:/srv/onpdb onpdb-environment get-bins: get-gnfinder get-gnverifier get-opsin get-gnfinder: ${BIN_PATH}/gnfinder get-gnverifier: ${BIN_PATH}/gnverifier get-opsin: ${BIN_PATH}/opsin-${OPSIN_VERSION}-jar-with-dependencies.jar bin/gnfinder: ${BIN_PATH}/gnfinder ${BIN_PATH}/gnfinder: config.mk mkdir -p bin ifeq (${PLATFORM},$(filter ${PLATFORM},mac linux)) curl -L https://github.com/gnames/gnfinder/releases/download/${GNFINDER_VERSION}/gnfinder-${GNFINDER_VERSION}-${PLATFORM}.tar.gz | tar xOz gnfinder > bin/gnfinder chmod +x bin/gnfinder else curl -L https://github.com/gnames/gnfinder/releases/download/${GNFINDER_VERSION}/gnfinder-${GNFINDER_VERSION}-win-64.zip > bin/gnfinder.zip unzip -o bin/gnfinder.zip -d bin/ rm bin/gnfinder.zip endif bin/gnverifier: ${BIN_PATH}/gnverifier ${BIN_PATH}/gnverifier: config.mk mkdir -p bin ifeq (${PLATFORM},$(filter ${PLATFORM},mac linux)) curl -L https://github.com/gnames/gnverifier/releases/download/${GNVERIFIER_VERSION}/gnverifier-${GNVERIFIER_VERSION}-${PLATFORM}.tar.gz | tar xOz gnverifier > bin/gnverifier chmod +x bin/gnverifier else curl -L https://github.com/gnames/gnverifier/releases/download/${GNVERIFIER_VERSION}/gnverifier-${GNVERIFIER_VERSION}-win-64.zip > bin/gnverifier.zip unzip -o bin/gnverifier.zip -d bin/ rm bin/gnverifier.zip endif bin/opsin-${OPSIN_VERSION}-jar-with-dependencies.jar: ${BIN_PATH}/opsin-${OPSIN_VERSION}-jar-with-dependencies.jar ${BIN_PATH}/opsin-${OPSIN_VERSION}-jar-with-dependencies.jar: config.mk mkdir -p bin curl -L https://github.com/dan2097/opsin/releases/download/${OPSIN_VERSION}/opsin-cli-${OPSIN_VERSION}-jar-with-dependencies.jar > bin/opsin-cli-${OPSIN_VERSION}-jar-with-dependencies.jar chmod +x bin/opsin-cli-${OPSIN_VERSION}-jar-with-dependencies.jar gathering-quick: gathering-custom-dictionaries gathering-translation-quick gathering-taxonomy-quick gathering-full: gathering-custom-dictionaries gathering-databases-full gathering-translation-full gathering-taxonomy-full gathering-full-hard: gathering-custom-dictionaries gathering-databases-full-hard gathering-translation-full gathering-taxonomy-full gathering-custom-dictionaries: make -C ${SRC_GATHERING_DICTIONARY_PATH} gathering-custom-dictionaries gathering-validation: make -C ${SRC_GATHERING_VALIDATION_PATH} gathering-validation gathering-databases-quick: gathering-databases-download gathering-databases-download-modified gathering-databases-accessible gathering-databases-full: gathering-databases-scrape gathering-databases-quick gathering-databases-full-hard: gathering-databases-semi gathering-databases-closed gathering-databases-full gathering-databases-accessible: mkdir -p ${INTERIM_DB_PATH} make -C ${SRC_GATHERING_DB_PATH} gathering-databases-accessible gathering-databases-semi: mkdir -p ${INTERIM_DB_PATH} make -C ${SRC_GATHERING_DB_PATH} gathering-databases-semi gathering-databases-closed: mkdir -p ${INTERIM_DB_PATH} make -C ${SRC_GATHERING_DB_PATH} gathering-databases-closed gathering-databases-download: ${DATABASES_DOWNLOAD} make -C ${SRC_GATHERING_DB_PATH} gathering-databases-download gathering-databases-download-modified: ${DATABASES_DOWNLOAD} make -C ${SRC_GATHERING_DB_PATH} gathering-databases-download-modified gathering-databases-scrape: ${DATABASES_SCRAPE} mkdir -p ${INTERIM_DB_PATH} make -C ${SRC_GATHERING_DB_PATH} gathering-databases-scrape gathering-translation-quick: gathering-translation-common-quick gathering-translation-tcm-quick gathering-translation-full: gathering-pmcid gathering-gbif gathering-chinese-board gathering-translation-tcmid gathering-translation-common gathering-translation-tcm gathering-translation-common: make -C ${SRC_GATHERING_TRANSLATION_PATH} gathering-translation-common gathering-translation-common-quick: make -C ${SRC_GATHERING_TRANSLATION_PATH} gathering-translation-common-quick gathering-translation-tcm: make -C ${SRC_GATHERING_TRANSLATION_PATH} gathering-translation-tcm gathering-translation-tcm-quick: make -C ${SRC_GATHERING_TRANSLATION_PATH} gathering-translation-tcm-quick gathering-translation-tcmid: make -C ${SRC_GATHERING_TRANSLATION_PATH} gathering-translation-tcmid gathering-gbif: make -C ${SRC_GATHERING_TRANSLATION_PATH} gathering-gbif gathering-chinese-board: make -C ${SRC_GATHERING_TRANSLATION_PATH} gathering-chinese-board gathering-pmcid: make -C ${SRC_GATHERING_TRANSLATION_PATH} gathering-pmcid gathering-taxonomy-full: gathering-taxonomy-npclassifier gathering-taxonomy-otl gathering-taxonomy-classyfire gathering-taxonomy-quick: gathering-taxonomy-npclassifier gathering-taxonomy-classyfire gathering-taxonomy-classyfire: make -C ${SRC_GATHERING_TAXONOMY_PATH} gathering-taxonomy-classyfire gathering-taxonomy-npclassifier: make -C ${SRC_GATHERING_TAXONOMY_PATH} gathering-taxonomy-npclassifier gathering-taxonomy-otl: make -C ${SRC_GATHERING_TAXONOMY_PATH} gathering-taxonomy-otl curating-and-analyzing-and-visualizing: curating analyzing visualizing curating-and-analyzing: curating analyzing curating: get-bins curating-1-integrating curating-editing curating-3-integrating curating-1-integrating: ${INTERIM_TABLE_ORIGINAL_PATH}/table.tsv.gz ${INTERIM_TABLE_ORIGINAL_PATH}/table.tsv.gz: ${DATABASES} paths.mk ${SRC_PATH}/paths.R ${SRC_CURATING_PATH}/1_integrating.R cd src && Rscript ${SRC_CURATING_PATH}/1_integrating.R curating-editing: curating-editing-structure curating-editing-organism curating-editing-reference curating-editing-structure: curating-editing-structure-translating curating-editing-structure-integrating curating-editing-structure-sanitizing curating-editing-structure-stereocounting curating-editing-structure-naming curating-editing-structure-classifying curating-editing-structure-translating: curating-editing-structure-translating-name curating-editing-structure-translating-inchi curating-editing-structure-translating-name: ${INTERIM_TABLE_TRANSLATED_STRUCTURE_PATH}/nominal.tsv.gz ${INTERIM_TABLE_TRANSLATED_STRUCTURE_PATH}/nominal.tsv.gz: ${SRC_CURATING_EDITING_STRUCTURE_TRANSLATING_PATH}/names.R ${INTERIM_TABLE_ORIGINAL_STRUCTURE_PATH}/nominal.tsv.gz cd src && Rscript ${SRC_CURATING_EDITING_STRUCTURE_TRANSLATING_PATH}/names.R curating-editing-structure-translating-inchi: ${INTERIM_TABLE_TRANSLATED_STRUCTURE_PATH}/inchi.tsv.gz ${INTERIM_TABLE_TRANSLATED_STRUCTURE_PATH}/inchi.tsv.gz: ${SRC_CURATING_EDITING_STRUCTURE_TRANSLATING_PATH}/inchi.py ${INTERIM_TABLE_ORIGINAL_STRUCTURE_PATH}/inchi.tsv.gz cd src && python ${SRC_CURATING_EDITING_STRUCTURE_TRANSLATING_PATH}/inchi.py ${INTERIM_TABLE_ORIGINAL_STRUCTURE_PATH}/inchi.tsv.gz ${INTERIM_TABLE_TRANSLATED_STRUCTURE_PATH}/inchi.tsv.gz structureOriginal_inchi curating-editing-structure-integrating: ${INTERIM_TABLE_TRANSLATED_STRUCTURE_PATH}/unique.tsv.gz ${INTERIM_TABLE_TRANSLATED_STRUCTURE_PATH}/unique.tsv.gz: ${SRC_CURATING_EDITING_STRUCTURE_PATH}/2_integrating.R ${INTERIM_TABLE_TRANSLATED_STRUCTURE_PATH}/inchi.tsv.gz ${INTERIM_TABLE_TRANSLATED_STRUCTURE_PATH}/nominal.tsv.gz ${INTERIM_TABLE_ORIGINAL_PATH}/table.tsv.gz cd src && Rscript ${SRC_CURATING_EDITING_STRUCTURE_PATH}/2_integrating.R curating-editing-structure-sanitizing: ${INTERIM_TABLE_PROCESSED_STRUCTURE_PATH}/processed.tsv.gz ${INTERIM_TABLE_PROCESSED_STRUCTURE_PATH}/processed.tsv.gz: ${SRC_CURATING_EDITING_STRUCTURE_PROCESSINGANDENRICHING_PATH}/chemosanitizer.py ${INTERIM_TABLE_TRANSLATED_STRUCTURE_PATH}/unique.tsv.gz cd src && python ${SRC_CURATING_EDITING_STRUCTURE_PROCESSINGANDENRICHING_PATH}/chemosanitizer.py ${INTERIM_TABLE_TRANSLATED_STRUCTURE_PATH}/unique.tsv.gz ${INTERIM_TABLE_PROCESSED_STRUCTURE_PATH}/processed.tsv.gz structureTranslated ${NPROCS} curating-editing-structure-stereocounting: ${INTERIM_TABLE_PROCESSED_STRUCTURE_PATH}/counted.tsv.gz ${INTERIM_TABLE_PROCESSED_STRUCTURE_PATH}/counted.tsv.gz: ${SRC_CURATING_EDITING_STRUCTURE_PROCESSINGANDENRICHING_PATH}/stereocounter.py ${INTERIM_TABLE_PROCESSED_STRUCTURE_PATH}/processed.tsv.gz cd src && python ${SRC_CURATING_EDITING_STRUCTURE_PROCESSINGANDENRICHING_PATH}/stereocounter.py ${INTERIM_TABLE_PROCESSED_STRUCTURE_PATH}/processed.tsv.gz ${INTERIM_TABLE_PROCESSED_STRUCTURE_PATH}/counted.tsv.gz smilesSanitized curating-editing-structure-naming: # add dependent files cd src && Rscript ${SRC_CURATING_EDITING_STRUCTURE_ENRICHING_PATH}/naming.R curating-editing-structure-classifying: # add dependent files cd src && Rscript ${SRC_CURATING_EDITING_STRUCTURE_ENRICHING_PATH}/np_classifier.R curating-editing-organism: curating-editing-organism-processing-original processing-organism-interim curating-editing-organism-translating curating-editing-organism-processing-translated curating-editing-organism-processing-taxonomy curating-editing-organism-processing-original: ${INTERIM_TABLE_PROCESSED_ORGANISM_PATH}/original.tsv.gz ${INTERIM_TABLE_PROCESSED_ORGANISM_PATH}/original.tsv.gz: $(wildcard ${INTERIM_TABLE_ORIGINAL_ORGANISM_PATH}/^[0-9]{6}.tsv) ${EXTERNAL_DICTIONARY_SOURCE_PATH}/taxa/ranks.tsv ${SRC_CURATING_EDITING_ORGANISM_PATH}/1_processingOriginal.R cd src && Rscript ${SRC_CURATING_EDITING_ORGANISM_PATH}/1_processingOriginal.R processing-organism-interim: @[ -f ${INTERIM_TABLE_PROCESSED_ORGANISM_PATH}/interim.tsv.gz ] && rm ${INTERIM_TABLE_PROCESSED_ORGANISM_PATH}/interim.tsv.gz || true cleaning-manual: @[ -d ${INTERIM_TABLE_PATH} ] && rm -r ${INTERIM_TABLE_PATH} || true @[ -d ${INTERIM_DICTIONARY_TEST_PATH} ] && rm -r ${INTERIM_DICTIONARY_TEST_PATH} || true curating-editing-organism-translating: ${INTERIM_TABLE_PROCESSED_ORGANISM_PATH}/interim.tsv.gz ${SRC_CURATING_EDITING_ORGANISM_PATH_KT}/build/libs/shadow.jar: ${SRC_CURATING_EDITING_ORGANISM_PATH_KT}/build.gradle.kts $(wildcard ${SRC_CURATING_EDITING_ORGANISM_PATH_KT}/src/main/kotlin/*.kt) ./gradlew castShadows ${INTERIM_TABLE_PROCESSED_ORGANISM_PATH}/interim.tsv.gz: ${INTERIM_TABLE_PROCESSED_ORGANISM_PATH}/original.tsv.gz ${EXTERNAL_DICTIONARY_SOURCE_PATH}/common/deny.tsv ${EXTERNAL_DICTIONARY_SOURCE_PATH}/common/manualSubtraction.tsv ${SRC_CURATING_EDITING_ORGANISM_PATH}/2_translating_organism_kotlin/build/libs/shadow.jar # ${EXTERNAL_DICTIONARY_SOURCE_PATH}/common/names.tsv.gz ${EXTERNAL_DICTIONARY_SOURCE_PATH}/tcm/names.tsv.gz @java -jar ${SRC_CURATING_EDITING_ORGANISM_PATH_KT}/build/libs/shadow.jar ${DATA_PATH} ${MODE} curating-editing-organism-processing-translated: curating-editing-organism-translating ${INTERIM_TABLE_PROCESSED_ORGANISM_PATH}/translated.tsv.gz ${INTERIM_TABLE_PROCESSED_ORGANISM_PATH}/translated.tsv.gz: ${INTERIM_TABLE_PROCESSED_ORGANISM_PATH}/original.tsv.gz ${EXTERNAL_DICTIONARY_SOURCE_PATH}/taxa/ranks.tsv ${SRC_CURATING_EDITING_ORGANISM_PATH}/3_processingTranslated.R cd src && Rscript ${SRC_CURATING_EDITING_ORGANISM_PATH}/3_processingTranslated.R curating-editing-organism-processing-taxonomy: ${INTERIM_TABLE_PROCESSED_ORGANISM_PATH}/processed.tsv.gz ${INTERIM_TABLE_PROCESSED_ORGANISM_PATH}/processed.tsv.gz: ${INTERIM_TABLE_PROCESSED_ORGANISM_PATH}/original.tsv.gz ${INTERIM_TABLE_PROCESSED_ORGANISM_PATH}/translated.tsv.gz ${SRC_CURATING_EDITING_ORGANISM_PATH}/4_processingTaxonomy.R cd src && Rscript ${SRC_CURATING_EDITING_ORGANISM_PATH}/4_processingTaxonomy.R curating-editing-reference: curating-editing-reference-translating curating-editing-reference-integrating curating-editing-reference-processing curating-editing-reference-translating: curating-editing-reference-translating-doi curating-editing-reference-translating-pubmed curating-editing-reference-translating-title curating-editing-reference-translating-split curating-editing-reference-translating-publishingDetails curating-editing-reference-translating-original curating-editing-reference-translating-doi: ${INTERIM_TABLE_TRANSLATED_REFERENCE_PATH}/doi.tsv.gz ${INTERIM_TABLE_TRANSLATED_REFERENCE_PATH}/doi.tsv.gz: ${SRC_CURATING_EDITING_REFERENCE_TRANSLATING_PATH}/doi.R ${INTERIM_TABLE_ORIGINAL_REFERENCE_PATH}/doi.tsv.gz cd src && Rscript ${SRC_CURATING_EDITING_REFERENCE_TRANSLATING_PATH}/doi.R curating-editing-reference-translating-pubmed: ${INTERIM_TABLE_TRANSLATED_REFERENCE_PATH}/pubmed.tsv.gz ${INTERIM_TABLE_TRANSLATED_REFERENCE_PATH}/pubmed.tsv.gz: ${SRC_CURATING_EDITING_REFERENCE_TRANSLATING_PATH}/pubmed.R ${INTERIM_TABLE_ORIGINAL_REFERENCE_PATH}/pubmed.tsv.gz cd src && Rscript ${SRC_CURATING_EDITING_REFERENCE_TRANSLATING_PATH}/pubmed.R curating-editing-reference-translating-title: ${INTERIM_TABLE_TRANSLATED_REFERENCE_PATH}/title.tsv.gz ${INTERIM_TABLE_TRANSLATED_REFERENCE_PATH}/title.tsv.gz: ${SRC_CURATING_EDITING_REFERENCE_TRANSLATING_PATH}/title.R $(wildcard ${INTERIM_TABLE_ORIGINAL_REFERENCE_PATH}/title/*.tsv.gz) cd src && Rscript ${SRC_CURATING_EDITING_REFERENCE_TRANSLATING_PATH}/title.R curating-editing-reference-translating-split: ${INTERIM_TABLE_TRANSLATED_REFERENCE_PATH}/split.tsv.gz ${INTERIM_TABLE_TRANSLATED_REFERENCE_PATH}/split.tsv.gz: ${SRC_CURATING_EDITING_REFERENCE_TRANSLATING_PATH}/split.R $(wildcard ${INTERIM_TABLE_ORIGINAL_REFERENCE_PATH}/split/*.tsv.gz) cd src && Rscript ${SRC_CURATING_EDITING_REFERENCE_TRANSLATING_PATH}/split.R curating-editing-reference-translating-publishingDetails: ${INTERIM_TABLE_TRANSLATED_REFERENCE_PATH}/publishingDetails.tsv.gz ${INTERIM_TABLE_TRANSLATED_REFERENCE_PATH}/publishingDetails.tsv.gz: ${SRC_CURATING_EDITING_REFERENCE_TRANSLATING_PATH}/publishingDetails.R $(wildcard ${INTERIM_TABLE_ORIGINAL_REFERENCE_PATH}/publishingDetails/*.tsv.gz) cd src && Rscript ${SRC_CURATING_EDITING_REFERENCE_TRANSLATING_PATH}/publishingDetails.R curating-editing-reference-translating-original: ${INTERIM_TABLE_TRANSLATED_REFERENCE_PATH}/original.tsv.gz ${INTERIM_TABLE_TRANSLATED_REFERENCE_PATH}/original.tsv.gz: ${SRC_CURATING_EDITING_REFERENCE_TRANSLATING_PATH}/original.R $(wildcard ${INTERIM_TABLE_ORIGINAL_REFERENCE_PATH}/original/*.tsv.gz) cd src && Rscript ${SRC_CURATING_EDITING_REFERENCE_TRANSLATING_PATH}/original.R curating-editing-reference-integrating: ${INTERIM_TABLE_TRANSLATED_REFERENCE_PATH}/integrated.tsv.gz ${INTERIM_TABLE_TRANSLATED_REFERENCE_PATH}/integrated.tsv.gz: ${SRC_CURATING_EDITING_REFERENCE_PATH}/2_integrating.R ${INTERIM_TABLE_TRANSLATED_REFERENCE_PATH}/doi.tsv.gz ${INTERIM_TABLE_TRANSLATED_REFERENCE_PATH}/pubmed.tsv.gz ${INTERIM_TABLE_TRANSLATED_REFERENCE_PATH}/title.tsv.gz ${INTERIM_TABLE_TRANSLATED_REFERENCE_PATH}/split.tsv.gz ${INTERIM_TABLE_TRANSLATED_REFERENCE_PATH}/original.tsv.gz ${INTERIM_TABLE_TRANSLATED_REFERENCE_PATH}/publishingDetails.tsv.gz ${INTERIM_TABLE_ORIGINAL_REFERENCE_PATH}/full.tsv.gz cd src && Rscript ${SRC_CURATING_EDITING_REFERENCE_PATH}/2_integrating.R curating-editing-reference-processing: ${INTERIM_TABLE_PROCESSED_REFERENCE_PATH}/processed.tsv.gz ${INTERIM_TABLE_PROCESSED_REFERENCE_PATH}/processed.tsv.gz: ${SRC_CURATING_EDITING_REFERENCE_PATH}/3_processing.R ${INTERIM_TABLE_TRANSLATED_REFERENCE_PATH}/integrated.tsv.gz # ${EXTERNAL_TRANSLATION_SOURCE_PATH}/pubmed/PMC-ids.csv.gz cd src && Rscript ${SRC_CURATING_EDITING_REFERENCE_PATH}/3_processing.R curating-3-integrating: ${INTERIM_TABLE_CURATED_PATH}/table.tsv.gz ${INTERIM_TABLE_CURATED_PATH}/table.tsv.gz: ${SRC_CURATING_PATH}/3_integrating.R ${INTERIM_TABLE_ORIGINAL_PATH}/table.tsv.gz ${INTERIM_TABLE_TRANSLATED_STRUCTURE_PATH}/inchi.tsv.gz ${INTERIM_TABLE_TRANSLATED_STRUCTURE_PATH}/nominal.tsv.gz ${INTERIM_TABLE_PROCESSED_STRUCTURE_PATH}/processed.tsv.gz ${INTERIM_TABLE_PROCESSED_ORGANISM_PATH}/processed.tsv.gz ${INTERIM_TABLE_PROCESSED_REFERENCE_PATH}/processed.tsv.gz cd src && Rscript ${SRC_CURATING_PATH}/3_integrating.R analyzing: gathering-validation analyzing-sampling analyzing-validating analyzing-metrics analyzing-examples analyzing-quick: gathering-validation analyzing-validating analyzing-sampling: # ${INTERIM_TABLE_CURATED_PATH}/table.tsv.gz cd src && Rscript ${SRC_ANALYSING_PATH}/1_sampling.R analyzing-validating: # ${INTERIM_TABLE_CURATED_PATH}/table.tsv.gz cd src && Rscript ${SRC_ANALYSING_PATH}/2_validating.R analyzing-metrics: # ${INTERIM_TABLE_CURATED_PATH}/table.tsv.gz cd src && Rscript ${SRC_ANALYSING_PATH}/3_metrics.R analyzing-examples: # ${INTERIM_TABLE_CURATED_PATH}/table.tsv.gz ${SRC_ANALYSING_PATH}/examples.R cd src && Rscript ${SRC_ANALYSING_PATH}/examples.R visualizing: visualizing-alluvial visualizing-chord visualizing-tree visualizing-upset visualizing-distribution visualizing-alluvial: cd src && Rscript ${SRC_VISUALIZING_PATH}/plot_alluvial.R visualizing-chord: cd src && Rscript ${SRC_VISUALIZING_PATH}/plot_chordDiagrams.R visualizing-tree: cd src && Rscript ${SRC_VISUALIZING_PATH}/plot_magicTree.R visualizing-upset: cd src && Rscript ${SRC_VISUALIZING_PATH}/plot_upset.R visualizing-distribution: cd src && Rscript ${SRC_VISUALIZING_PATH}/plot_distribution.R lotus-bloom: cleaning-manual gathering-quick curating analyzing-quick lotus-seeds: gathering-full curating analyzing visualizing lotus-roots: gathering-full-hard curating analyzing visualizing lotus-check: cd src && Rscript ${TESTS_PATH}/tests.R