README.Rmd

---
output:
  github_document:
    toc: true

---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = FALSE,
  comment = "",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# 📚 gpgr - Genomics Platform Group Reporting

Contains reports and functions used in the Genomics Platform Group
at the University of Melbourne Centre for Cancer Research.

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

[![Conda install](https://anaconda.org/umccr/r-gpgr/badges/version.svg)](https://anaconda.org/umccr/r-gpgr)
[![Conda install](https://anaconda.org/umccr/r-gpgr/badges/latest_release_date.svg)](https://anaconda.org/umccr/r-gpgr)

## Installation

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

- Or if used inside a conda environment:

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

## Main modules

### 🔮 PURPLE {#id_-purple}

- Read and process output files from the `PURPLE` purity/copy number estimator
  tool from the Hartwig Medical Foundation
  (<https://github.com/hartwigmedical/hmftools/tree/master/purple>).
  See vignette at <https://umccr.github.io/gpgr/articles/purple.html>.

### 🐍 umccrise {#id_-umccrise}

- Generate a HTML report with results from the `umccrise` DRAGEN tumor/normal
  post-processing workflow from UMCCR - <https://github.com/umccr/umccrise>.
  See the [CLI](#cli) section below for options.

## 🥳 Developers {#id_-developers}

See <https://umccr.github.io/gpgr/articles/devnotes.html> for developer notes.

## 💻 CLI {#id_-cli}

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

- If you're using the conda package, the `gpgr.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
  `gpgr/inst/cli/` directory to your `PATH` in order to use `gpgr.R`.

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

```{bash prompt=TRUE, echo=FALSE}
gpgr_cli=$(Rscript -e 'x = system.file("cli", package = "gpgr"); cat(x, "\n")' | xargs)
export PATH="${gpgr_cli}:${PATH}"
echo "gpgr.R --version" & gpgr.R --version
echo ""
echo "#-----------------------------------#"
echo "gpgr.R --help" & gpgr.R --help
echo ""
echo "#-----------------------------------#"
echo "#------- Cancer Report -------#"
echo "gpgr.R canrep --help" & gpgr.R canrep --help
echo ""
echo "#-----------------------------------#"
```