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Makefile
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################################################################################
# COMMANDS #
################################################################################
.PHONY: qa
## Apply code quality assurance tools.
qa:
isort src/taxpasta tests/
black src/taxpasta tests/
.PHONY: docs
## Generate documentation
docs: qmd
taxpasta standardise --help > docs/quick_reference/standardise_help.txt
taxpasta merge --help > docs/quick_reference/merge_help.txt
tutorial_snippets := $(patsubst %.qmd,%.md,$(wildcard docs/tutorials/*.qmd))
howto_snippets := $(patsubst %.qmd,%.md,$(wildcard docs/how-tos/*.qmd))
snippets := $(tutorial_snippets) $(howto_snippets)
qmd: profiles $(snippets)
%.md: %.qmd
# Requires installation of quarto https://quarto.org/docs/get-started/
# and the bash kernel `python -m bash_kernel.install`.
quarto render $<
profiles: docs/tutorials/2612_pe-ERR5766176-db1_kraken2.tsv docs/tutorials/dbMOTUs_motus.tsv docs/tutorials/2612_pe-ERR5766176-db_mOTU.out docs/tutorials/2612_se-ERR5766180-db_mOTU.out docs/tutorials/2612_pe-ERR5766176-db1.kraken2.report.txt
docs/tutorials/2612_pe-ERR5766176-db1_kraken2.tsv: docs/tutorials/2612_pe-ERR5766176-db1.kraken2.report.txt
cd docs/tutorials && taxpasta standardise -p kraken2 -o 2612_pe-ERR5766176-db1_kraken2.tsv 2612_pe-ERR5766176-db1.kraken2.report.txt
docs/tutorials/dbMOTUs_motus.tsv: docs/tutorials/2612_pe-ERR5766176-db_mOTU.out docs/tutorials/2612_se-ERR5766180-db_mOTU.out
cd docs/tutorials && taxpasta merge -p motus -o dbMOTUs_motus.tsv 2612_pe-ERR5766176-db_mOTU.out 2612_se-ERR5766180-db_mOTU.out
docs/tutorials/2612_pe-ERR5766176-db_mOTU.out:
cd docs/tutorials && curl -O https://raw.githubusercontent.com/taxprofiler/taxpasta/dev/tests/data/motus/2612_pe-ERR5766176-db_mOTU.out
docs/tutorials/2612_se-ERR5766180-db_mOTU.out:
cd docs/tutorials && curl -O https://raw.githubusercontent.com/taxprofiler/taxpasta/dev/tests/data/motus/2612_se-ERR5766180-db_mOTU.out
docs/tutorials/2612_pe-ERR5766176-db1.kraken2.report.txt:
cd docs/tutorials && curl -O https://raw.githubusercontent.com/taxprofiler/taxpasta/dev/tests/data/kraken2/2612_pe-ERR5766176-db1.kraken2.report.txt
taxonomy_directory := tests/data/taxonomy
## Generate test files
test-setup: $(taxonomy_directory)
# Running this command assumes that the taxonkit
# (https://bioinf.shenwei.me/taxonkit/) has been installed beforehand and the
# NCBI taxonomy was downloaded.
$(taxonomy_directory):
taxonkit list --ids '160488,511145,889517' --indent "" \
| taxonkit reformat --taxid-field 1 --output-ambiguous-result --format "{k}\t{p}\t{c}\t{o}\t{f}\t{g}\t{s}" \
| cut --fields=2-8 \
| taxonkit create-taxdump --out-dir "$(taxonomy_directory)" --force --rank-names "superkingdom,phylum,class,order,family,genus,species"
################################################################################
# Self Documenting Commands #
################################################################################
.DEFAULT_GOAL := show-help
# Inspired by
# <http://marmelab.com/blog/2016/02/29/auto-documented-makefile.html>
# sed script explained:
# /^##/:
# * save line in hold space
# * purge line
# * Loop:
# * append newline + line to hold space
# * go to next line
# * if line starts with doc comment, strip comment character off and loop
# * remove target prerequisites
# * append hold space (+ newline) to line
# * replace newline plus comments by `---`
# * print line
# Separate expressions are necessary because labels cannot be delimited by
# semicolon; see <http://stackoverflow.com/a/11799865/1968>
.PHONY: show-help
show-help:
@echo "$$(tput bold)Available rules:$$(tput sgr0)"
@echo
@sed -n -e "/^## / { \
h; \
s/.*//; \
:doc" \
-e "H; \
n; \
s/^## //; \
t doc" \
-e "s/:.*//; \
G; \
s/\\n## /---/; \
s/\\n/ /g; \
p; \
}" ${MAKEFILE_LIST} \
| LC_ALL='C' sort --ignore-case \
| awk -F '---' \
-v ncol=$$(tput cols) \
-v indent=19 \
-v col_on="$$(tput setaf 6)" \
-v col_off="$$(tput sgr0)" \
'{ \
printf "%s%*s%s ", col_on, -indent, $$1, col_off; \
n = split($$2, words, " "); \
line_length = ncol - indent; \
for (i = 1; i <= n; i++) { \
line_length -= length(words[i]) + 1; \
if (line_length <= 0) { \
line_length = ncol - indent - length(words[i]) - 1; \
printf "\n%*s ", -indent, " "; \
} \
printf "%s ", words[i]; \
} \
printf "\n"; \
}' \
| more $(shell test $(shell uname) = Darwin && \
echo '--no-init --raw-control-chars')