<commit_before>#!/bin/bash

if [ "$EUID" -ne 0 ]; then
  echo "This script must be run as root"
  exit
fi


# Pandoc (markup tool) install
echo "Downloading and installing Pandoc v.1.17.1-2 \n PLEASE CHECK that this is the most recent stable release."
wget http://github.com/jgm/pandoc/releases/download/1.17.1/pandoc-1.17.1-2-amd64.deb
dpkg -i pandoc-1.17.1-2-amd64.deb


# RStudio IDE install
echo "Downloading and installing RStudio v.0,99.902 \n PLEASE CHECK that this is the most recent stable release."
wget https://download1.rstudio.org/rstudio-0.99.902-amd64.deb
dpkg -i rstudio-0.99.902-amd64.deb


# add some global tools from Node.js
npm install -g diff-so-fancy  #much prettier git diffs
npm install -g how2  #use StackOverflow from command line


# add SSH tools for remote access
#apt-get install openssh-server


# add command line tools for Genomics
apt-get install samtools  #for genomic alignments
apt-get install bedtools  #for genomic annotation


# fix installation issues arising from dependencies
apt-get install -f<commit_msg>add hpm for HyperTerm<commit_after>#!/bin/bash

if [ "$EUID" -ne 0 ]; then
  echo "This script must be run as root"
  exit
fi


# Pandoc (markup tool) install
echo "Downloading and installing Pandoc v.1.17.1-2 \n PLEASE CHECK that this is the most recent stable release."
wget http://github.com/jgm/pandoc/releases/download/1.17.1/pandoc-1.17.1-2-amd64.deb
dpkg -i pandoc-1.17.1-2-amd64.deb


# RStudio IDE install
echo "Downloading and installing RStudio v.0,99.902 \n PLEASE CHECK that this is the most recent stable release."
wget https://download1.rstudio.org/rstudio-0.99.902-amd64.deb
dpkg -i rstudio-0.99.902-amd64.deb


# add some global tools from Node.js
npm install -g diff-so-fancy  #much prettier git diffs
npm install -g how2  #use StackOverflow from command line
npm install -g hpm-cli  #package/plug-in manager for Hyperterm


# add SSH tools for remote access
#apt-get install openssh-server


# add command line tools for Genomics
apt-get install samtools  #for genomic alignments
apt-get install bedtools  #for genomic annotation


# fix installation issues arising from dependencies
apt-get install -f
{'fraction_non_alphanumeric': 0.0916628281897743, 'fraction_numerical': 0.044219253800092125, 'mean_word_length': 3.794701986754967, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 8, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6111307', 'n_tokens_mistral': 819, 'n_tokens_neox': 719, 'n_words': 262}