Add pipeline selector landing page, rewrite getting started, fix stale doc paths - #1397
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jaempawi wants to merge 11 commits into
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Add pipeline selector landing page, rewrite getting started, fix stale doc paths#1397jaempawi wants to merge 11 commits into
jaempawi wants to merge 11 commits into
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Documented sos run examples pointed at personal checkouts (~/codes/xqtl-protocol/, /home/hs3163/GIT/xqtl-protocol/, ~/GIT/xqtl-protocol/), so they could only work for their author. Replaced the prefixes with plain pipeline/ paths. No other path classes touched.
Answers "which pipelines do I need" from a few questions about the user data, then lists the applicable pipelines with inputs, outputs and commands. High-dimensional Regression is organised by data level (individual vs summary statistics), with fine-mapping and TWAS weights as products of the same run per Gao. RSS TWAS weights and scEEMS Prediction are marked as not yet wired into SoS.
…atFunGen#1393 genotype_formatting.py, bulk_expression_normalization.py and RNA_calling.py were ported to R and deleted, so the README verification snippet failed at the first step.
MRAID_QTL and polyfun are deprecated; no need to rewrite their paths.
Three references read pipeline/pipeline/reference_data.ipynb; pipelines are run as pipeline/<name>.ipynb from the repo root.
build_flat_book.py collects *.ipynb from code/SoS as pages and copies other files there as assets; a file at the repo root is not staged.
Jupyter Book only builds documents listed in _toc.yml (only_build_toc_files: true) and cannot render a raw .html as a page, so the selector is wrapped in a notebook with the markup in a markdown cell.
Removes the conda step: pixi-setup already provides sos, jupyter and a registered sos kernel, and the old advice to conda activate sos pointed users away from the environment holding plink/samtools/tensorqtl. Fixes the installer command: piped into bash the two prompts consume nothing, so users silently got a minimal install. Download then run instead. Replaces the Synapse download with tests/fixtures/, which ships in the repo, and links the pipeline selector.
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What this adds
1. An interactive pipeline selector, added to the book under Getting started
(
code/SoS/xqtl_protocol_landing_page.ipynb). It answers the question the docsdon't answer directly: which pipelines do I need?
2. A rewritten getting-started page (
code/SoS/xqtl_protocol_demo.ipynb).Documentation fixes included
code/snakemake/README.md— thepy_compilesnippet listed three files removedin add many more tests and R ports #1393 (
genotype_formatting.py,bulk_expression_normalization.py,RNA_calling.py), so it failed at the first step. Verified the remaining commandruns (
python -m py_compile … && echo $?→ 0).bulk_expression_commands.ipynb— three references readpipeline/pipeline/reference_data.ipynb. Pre-existing onmain; pipelines run aspipeline/<name>.ipynbfrom the repo root.bulk_expression_commands.ipynb,eQTL_analysis_commands.ipynb,METAL_pipeline.ipynb— documented commands pointed at personal checkouts(
~/codes/xqtl-protocol/,/home/hs3163/GIT/xqtl-protocol/), so they only workedfor their author. Now repo-relative. Deprecated notebooks under
graveyard/leftuntouched.