From 3bd826d237391d292622f0ae96aa66c25911bb19 Mon Sep 17 00:00:00 2001 From: Jerome Kelleher Date: Thu, 9 May 2024 23:43:43 +0100 Subject: [PATCH 1/2] First pass at executable tutorial --- .github/workflows/docs.yml | 9 +++++++-- docs/_toc.yml | 1 + docs/requirements.txt | 3 ++- docs/vcf2zarr_tutorial.md | 28 ++++++++++++++++++++++++++++ 4 files changed, 38 insertions(+), 3 deletions(-) create mode 100644 docs/vcf2zarr_tutorial.md diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 4c6f2796..40986574 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -1,4 +1,4 @@ -name: Build Docs +name: Docs on: pull_request: @@ -10,7 +10,7 @@ on: jobs: build-docs: - name: Docs + name: Build runs-on: ubuntu-latest steps: - name: Cancel Previous Runs @@ -29,6 +29,11 @@ jobs: run: | pip install --upgrade pip wheel pip install -r docs/requirements.txt + python3 -m bash_kernel.install + + - name: Install package + run: | + python3 -m pip install . - name: Build Docs run: | diff --git a/docs/_toc.yml b/docs/_toc.yml index d6e492ca..008d36ff 100644 --- a/docs/_toc.yml +++ b/docs/_toc.yml @@ -1,4 +1,5 @@ format: jb-book root: intro chapters: +- file: vcf2zarr_tutorial - file: cli diff --git a/docs/requirements.txt b/docs/requirements.txt index 0eb2c5c4..af9c16f0 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,3 +1,4 @@ +bash_kernel bed_reader click cyvcf2 @@ -8,4 +9,4 @@ sgkit sphinx-click tabulate tqdm -zarr>=2.17 \ No newline at end of file +zarr>=2.17 diff --git a/docs/vcf2zarr_tutorial.md b/docs/vcf2zarr_tutorial.md new file mode 100644 index 00000000..a3048c29 --- /dev/null +++ b/docs/vcf2zarr_tutorial.md @@ -0,0 +1,28 @@ +--- +jupytext: + formats: md:myst + text_representation: + extension: .md + format_name: myst +kernelspec: + display_name: Bash + language: bash + name: bash +--- +# Vcf2zarr tutorial + +This is a step-by-step tutorial showing you how to convert your +VCF data into Zarr format. There's three different ways to +convert your data, basically providing different levels of +convenience and flexibility corresponding to what you might +need for small, intermediate and large datasets. + +## Small + +```{code-cell} bash +vcf2zarr convert ../tests/data/vcf/sample.vcf.gz sample.zarr -vf +``` + +## Intermediate + +## Large From dffea3d78e76ebcdf34f82249bc7f1e439c8f145 Mon Sep 17 00:00:00 2001 From: Jerome Kelleher Date: Thu, 9 May 2024 23:47:58 +0100 Subject: [PATCH 2/2] Trim docs requirements. --- docs/requirements.txt | 9 --------- 1 file changed, 9 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index af9c16f0..4843775a 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,12 +1,3 @@ bash_kernel -bed_reader -click -cyvcf2 jupyter-book -msprime -pysam -sgkit sphinx-click -tabulate -tqdm -zarr>=2.17