<commit_before>#!/bin/bash

done_message () {
  set +e
    if [ $? -eq 0 ]; then
        echo " done."
        if [ "x$1" != "x" ]; then
            echo $1
        fi
    else
        echo " failed.  See setup.log file for error messages." $2
        echo "    Please check INSTALL file for items that should be installed by a package manager"
        exit 1
    fi
  set -e
}

get_distro () {
  set +e
  if hash curl 2>/dev/null; then
    curl -sS -o current.tar.gz -L $1
  else
    wget -nv -O current.tar.gz $1
  fi
  set -e
  mkdir -p current
  tar --strip-components 1 -C current -zxf current.tar.gz
}

repos=(
  "https://github.com/ICGC-TCGA-PanCancer/PCAP-core/archive/v1.2.3.tar.gz"
  "https://github.com/cancerit/cgpVcf/archive/v1.2.2.tar.gz"
  "https://github.com/cancerit/alleleCount/archive/v1.2.1.tar.gz"
  "https://github.com/cancerit/cgpBinCounts/archive/v1.0.0.tar.gz"
  "https://github.com/cancerit/cgpNgsQc/archive/v0.0.1-dev.tar.gz"
  "https://github.com/cancerit/ascatNgs/archive/v1.5.0.tar.gz"
  "https://github.com/cancerit/cgpPindel/archive/v1.1.2.tar.gz"
  "https://github.com/cancerit/cgpCaVEManPostProcessing/archive/v1.0.2.tar.gz"
  "https://github.com/cancerit/cgpCaVEManWrapper/archive/v1.2.0.tar.gz"
  "https://github.com/cancerit/BRASS/archive/v2.1.0.tar.gz"
  "https://github.com/cancerit/VAGrENT/archive/v2.0.0.tar.gz"
  "https://github.com/cancerit/grass/archive/v1.0.1.tar.gz"
 )

# clear log file
INIT_DIR=$(dirname $(readlink -f $0))
echo > $INIT_DIR/setup.log
set -eu

for i in "${repos[@]}" ; do
  echo -n "Installing $i..."
  (
    get_distro $i<commit_msg>Missed version change in cgpNgsQc<commit_after>#!/bin/bash

done_message () {
  set +e
    if [ $? -eq 0 ]; then
        echo " done."
        if [ "x$1" != "x" ]; then
            echo $1
        fi
    else
        echo " failed.  See setup.log file for error messages." $2
        echo "    Please check INSTALL file for items that should be installed by a package manager"
        exit 1
    fi
  set -e
}

get_distro () {
  set +e
  if hash curl 2>/dev/null; then
    curl -sS -o current.tar.gz -L $1
  else
    wget -nv -O current.tar.gz $1
  fi
  set -e
  mkdir -p current
  tar --strip-components 1 -C current -zxf current.tar.gz
}

repos=(
  "https://github.com/ICGC-TCGA-PanCancer/PCAP-core/archive/v1.2.3.tar.gz"
  "https://github.com/cancerit/cgpVcf/archive/v1.2.2.tar.gz"
  "https://github.com/cancerit/alleleCount/archive/v1.2.1.tar.gz"
  "https://github.com/cancerit/cgpBinCounts/archive/v1.0.0.tar.gz"
  "https://github.com/cancerit/cgpNgsQc/archive/v1.0.0.tar.gz"
  "https://github.com/cancerit/ascatNgs/archive/v1.5.0.tar.gz"
  "https://github.com/cancerit/cgpPindel/archive/v1.1.2.tar.gz"
  "https://github.com/cancerit/cgpCaVEManPostProcessing/archive/v1.0.2.tar.gz"
  "https://github.com/cancerit/cgpCaVEManWrapper/archive/v1.2.0.tar.gz"
  "https://github.com/cancerit/BRASS/archive/v2.1.0.tar.gz"
  "https://github.com/cancerit/VAGrENT/archive/v2.0.0.tar.gz"
  "https://github.com/cancerit/grass/archive/v1.0.1.tar.gz"
 )

# clear log file
INIT_DIR=$(dirname $(readlink -f $0))
echo > $INIT_DIR/setup.log
set -eu

for i in "${repos[@]}" ; do
  echo -n "Installing $i..."
  (
    get_distro $i
{'fraction_non_alphanumeric': 0.1727895392278954, 'fraction_numerical': 0.028642590286425903, 'mean_word_length': 2.5859375, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 7, 'https://': 24, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6921654', 'n_tokens_mistral': 1383, 'n_tokens_neox': 1340, 'n_words': 233}