README.Rmd

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# 🎶 sigrap {#id_-sigrap}

Wrappers for somatic mutation signature analysis tools
(HRDetect, CHORD, MutationalPatterns).

- Docs: <https://umccr.github.io/sigrap/>

<!-- badges: start -->
[![Conda install](https://anaconda.org/umccr/r-sigrap/badges/installer/conda.svg)](https://anaconda.org/umccr/r-sigrap)
<!-- badges: end -->

## Installation

```r
remotes::install_github("umccr/sigrap")
```

- Or if used inside a conda environment:

```bash
conda install r-sigrap -c umccr -c conda-forge -c bioconda
```

## Main Modules

### 🔍 HRDetect {#id_-hrdetect}

Wraps functionality from the [HRDetect](https://github.com/Nik-Zainal-Group/signature.tools.lib)
framework - see
vignette at <https://umccr.github.io/sigrap/articles/hrdetect.html>.

### 🎸 CHORD {#id_-chord}

Wraps functionality from [CHORD](https://github.com/UMCUGenetics/CHORD) - see
vignette at <https://umccr.github.io/sigrap/articles/chord.html>.

### 🐾 MutationalPatterns {#id_-mutationalpatterns}

Wraps functionality from [MutationalPatterns](https://github.com/UMCUGenetics/MutationalPatterns) - see
vignette at <https://umccr.github.io/sigrap/articles/mutationalpatterns.html>.

## 💻 CLI {#id_-cli}

A `sigrap` command line interface is available for convenience.

- If you're using the conda package, the `sigrap.R` command will already be set up
  inside an activated conda environment.
- If you're _not_ using the conda package, you need to export the
  `sigrap/inst/cli/` directory to your `PATH` in order to use `sigrap.R`.

```{bash echo=TRUE, eval=FALSE}
sigrap_cli=$(Rscript -e 'x = system.file("cli", package = "sigrap"); cat(x, "\n")' | xargs)
export PATH="${sigrap_cli}:${PATH}"
```

```{bash prompt=TRUE, echo=FALSE}
sigrap_cli=$(Rscript -e 'x = system.file("cli", package = "sigrap"); cat(x, "\n")' | xargs)
export PATH="${sigrap_cli}:${PATH}"

echo "sigrap.R --version" & sigrap.R --version
echo ""
echo "#-----------------------------------#"
echo "sigrap.R --help" & sigrap.R --help
echo ""
echo "#------- HRDetect -------#"
echo "sigrap.R hrdetect --help" & sigrap.R hrdetect --help
echo ""
echo "#------- CHORD -------#"
echo "sigrap.R chord --help" & sigrap.R chord --help
echo ""
echo "#------- MutationalPatterns -------#"
echo ""
echo "sigrap.R mutpat --help" & sigrap.R mutpat --help
```