diff --git a/docs/Makefile b/docs/Makefile index 623d123..e830590 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -3,12 +3,16 @@ PYPATH=$(shell pwd)/../ B2Z_VERSION:=$(shell PYTHONPATH=${PYPATH} \ python3 -c 'import bio2zarr; print(bio2zarr.__version__.split("+")[0])') +CASTS=_static/vcf2zarr_convert.cast\ + _static/vcf2zarr_explode.cast + + BUILDDIR = _build -dev: _static/vcf2zarr_convert.cast +dev: ${CASTS} PYTHONPATH=${PYPATH} ./build.sh -dist: _static/vcf2zarr_convert.cast +dist: ${CASTS} @echo Building distribution for bio2zarr version ${B2Z_VERSION} cd doxygen && doxygen sed -i -e s/__BIO2ZARR_VERSION__/${B2Z_VERSION}/g _config.yml @@ -18,8 +22,15 @@ clean: rm -fR $(BUILDDIR) -_static/vcf2zarr_convert.cast: - rm -fR sample.zarr +sample.vcf.gz: cp ../tests/data/vcf/sample.vcf.gz ./ cp ../tests/data/vcf/sample.vcf.gz.tbi ./ - asciinema-automation cast_scripts/vcf2zarr_convert.sh _static/vcf2zarr_convert.cast + +_static/vcf2zarr_convert.cast: sample.vcf.gz + rm -f sample.vcz + asciinema-automation cast_scripts/vcf2zarr_convert.sh $@ + +_static/vcf2zarr_explode.cast: sample.vcf.gz + rm -Rf sample.icf + asciinema-automation cast_scripts/vcf2zarr_explode.sh $@ + diff --git a/docs/cast_scripts/vcf2zarr_convert.sh b/docs/cast_scripts/vcf2zarr_convert.sh index 7ada9c7..8741fa8 100644 --- a/docs/cast_scripts/vcf2zarr_convert.sh +++ b/docs/cast_scripts/vcf2zarr_convert.sh @@ -1,3 +1,3 @@ -#$ delay 10 -vcf2zarr convert sample.vcf.gz sample.zarr -p 4 +#$ delay 5 +vcf2zarr convert sample.vcf.gz sample.vcz #$ expect \$ diff --git a/docs/cast_scripts/vcf2zarr_explode.sh b/docs/cast_scripts/vcf2zarr_explode.sh new file mode 100644 index 0000000..37be934 --- /dev/null +++ b/docs/cast_scripts/vcf2zarr_explode.sh @@ -0,0 +1,3 @@ +#$ delay 5 +vcf2zarr explode sample.vcf.gz sample.icf +#$ expect \$ diff --git a/docs/vcf2zarr/tutorial.md b/docs/vcf2zarr/tutorial.md index 223bb15..7f6dbff 100644 --- a/docs/vcf2zarr/tutorial.md +++ b/docs/vcf2zarr/tutorial.md @@ -20,10 +20,6 @@ need for small, intermediate and large datasets. ## Small - - - -
+ + ## Large