00_packageVersions.Rmd

---
title: "Bender et al (2024) -- EMBO"
subtitle: Package versions
author:
- name: Alexander Bender
  affiliation: Institute of Molecular Tumor Biology, Muenster/Germany
date: "`r paste('Compiled:', format(Sys.time(), '%d-%b-%Y'))`"
output:
  rmdformats::readthedown:
    code_folding: show
    keep_md: false
    highlight: tango
    toc_float:
      collapsed: false
editor_options: 
  markdown: 
    wrap: 200
---

<style>
body {
text-align: justify}
</style>

# Setup

Define root directory that contains the folder with source data. Run script that
loads packages and define document-specific variables.

```{r setup}

# Inside this Docker container we mount the directory with all the source data as "/projectdir/"
rootdir <- "/projectdir/"
source(paste0(rootdir, "/runStartup.R"))
```

# Package versions

A summary of all R package versions installed in this container:

```{r pkgs}

pkg_ver <-
  lapply(rownames(installed.packages()), function(x) {
    data.frame(package = x, version = packageVersion(x))
  }) %>%
  do.call(rbind, .) %>%
  dplyr::arrange(package) %>%
  unique()

knitr::kable(pkg_ver)

sessionInfo()
```

# Command line tools

Versions of MAGeCK RRA, meme, homer, bedtools

```{bash}

echo "ame:" $(/software/meme/bin/ame --version)
echo "bedtools:" $(/software/bedtools2/bin/bedtools --version | awk '{gsub("bedtools ", "");print}')
echo "mageck:" "$(${MAGECKPATH}/mageck --version)"
echo "meme:" $(/software/meme/bin/meme -version)
```