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Usage Guide

Installation

Recommended setup:

python3 -m venv .venv
source .venv/bin/activate
python -m pip install --upgrade pip
pip install -e .[dev]

If you want a runtime-only install without test dependencies:

pip install .

Repository-local launcher

From a repository checkout, you can use:

./rnaconsnake-run --version

It automatically prefers ./.venv/bin/python when present and otherwise falls back to python3.

Dependency checks

Check the standard runtime dependencies:

rnaconsnake-run --check-deps

Check the dependency set including optional R-scape support:

rnaconsnake-run --check-deps --rscape

To inspect which external tool commands RNAConSnake is configured to use, and where their executables resolve on the current machine:

rnaconsnake-run --show-tool-paths

Basic run

rnaconsnake-run --input-alignment /path/to/my_alignment.stk --cores all

To write all outputs into a dedicated working directory:

rnaconsnake-run --input-alignment /path/to/my_alignment.stk --output-dir /path/to/run_dir --cores all

Common options

Override the default maxbpspan values:

rnaconsnake-run --input-alignment /path/to/my_alignment.stk --maxbpspan 150 --maxbpspan 250 --cores all

Enable optional per-hit R-scape analysis:

rnaconsnake-run --input-alignment /path/to/my_alignment.stk --rscape --cores all

RNAz defaults to -d -n, which disables alignment shuffling. To explicitly allow shuffling:

rnaconsnake-run --input-alignment /path/to/my_alignment.stk --rnaz-shuffle --cores all

If you want Snakemake to reuse existing outputs more conservatively and avoid reruns caused only by workflow code changes:

rnaconsnake-run --conservative --cores all

Structured export

RNAConSnake can generate a structured export bundle after a successful run:

rnaconsnake-run \
  --input-alignment /path/to/my_alignment.stk \
  --output-dir /path/to/run_dir \
  --export-bundle /path/to/export_bundle \
  --cores all

You can also override export metadata, for example:

rnaconsnake-run \
  --input-alignment /path/to/my_alignment.stk \
  --output-dir /path/to/run_dir \
  --export-bundle /path/to/export_bundle \
  --export-feature-type other \
  --export-feature-label "Example aligned feature" \
  --export-dataset-label "Example dataset" \
  --cores all

Configuration

The default workflow configuration lives in ../config.yaml.

Useful preprocessing settings include:

remove_gaponly_gapratio: 0.5
remove_gaponly_max_n: 0
do_rscape: false
rnaz_no_shuffle: true

Meaning:

  • remove_gaponly_gapratio Maximum allowed gap fraction per sequence in the split Stockholm alignment.
  • remove_gaponly_max_n Maximum allowed count of N or n characters per sequence. 0 means sequences containing any N/n are removed.
  • rnaz_no_shuffle Controls whether RNAz is called with -n. The default is true, which disables alignment shuffling.

Example:

remove_gaponly_max_n: 2

Cleaning outputs

To remove generated workflow outputs from a run directory:

snakemake --cores 1 clean

or:

rm -rf Lalifold generated_files