<commit_before>#!/usr/bin/env bash

set -e # Exit as soon as any line in the bash script fails

ROOTDIR=$( cd $(dirname $0) ; pwd -P ) # path to main PiReT directory


echo
exec &> >(tee -a  install.log)
exec 2>&1 # copies stderr onto stdout

# create a directory where all dependencies will be installed
cd $ROOTDIR
mkdir -p thirdParty
cd thirdParty


# create a directory to add short cuts to dependencies
mkdir -p $ROOTDIR/bin
export "PATH=$PATH:$ROOTDIR/bin/"
if [[ "$OSTYPE" == "darwin"* ]]
then
{
export PERL5LIB="$ROOTDIR/ext/lib/perl5:$ROOTDIR/ext/lib/perl5/darwin-thread-multi-2level:$PERL5LIB"
}
else
#TODO: update this specific to unix
{  
export PERL5LIB="$ROOTDIR/ext/lib/perl5:$ROOTDIR/lib/perl5/darwin-thread-multi-2level/:$PERL5LIB"
}
fi

# Add pythonpath
# export PYTHONPATH="$ROOTDIR/thirdParty/miniconda/lib/python2.7/site-packages/:$PYTHONPATH"

#Add R path
export R_LIBS="$ROOTDIR/ext/lib/R:$R_LIBS:$R_LIBS_USER"

# Minimum Required versions of dependencies
cpanm_VER=1.7039
miniconda_VER=4.2.12
samtools_VER=1.3.1
bamtools_VER=2.4.0<commit_msg>updated the version of miniconda as it was being updated when instaling R<commit_after>#!/usr/bin/env bash

set -e # Exit as soon as any line in the bash script fails

ROOTDIR=$( cd $(dirname $0) ; pwd -P ) # path to main PiReT directory


echo
exec &> >(tee -a  install.log)
exec 2>&1 # copies stderr onto stdout

# create a directory where all dependencies will be installed
cd $ROOTDIR
mkdir -p thirdParty
cd thirdParty


# create a directory to add short cuts to dependencies
mkdir -p $ROOTDIR/bin
export "PATH=$PATH:$ROOTDIR/bin/"
if [[ "$OSTYPE" == "darwin"* ]]
then
{
export PERL5LIB="$ROOTDIR/ext/lib/perl5:$ROOTDIR/ext/lib/perl5/darwin-thread-multi-2level:$PERL5LIB"
}
else
#TODO: update this specific to unix
{  
export PERL5LIB="$ROOTDIR/ext/lib/perl5:$ROOTDIR/lib/perl5/darwin-thread-multi-2level/:$PERL5LIB"
}
fi

# Add pythonpath
# export PYTHONPATH="$ROOTDIR/thirdParty/miniconda/lib/python2.7/site-packages/:$PYTHONPATH"

#Add R path
export R_LIBS="$ROOTDIR/ext/lib/R:$R_LIBS:$R_LIBS_USER"

# Minimum Required versions of dependencies
cpanm_VER=1.7039
miniconda_VER=4.3.21
samtools_VER=1.3.1
bamtools_VER=2.4.0
{'fraction_non_alphanumeric': 0.12773722627737227, 'fraction_numerical': 0.02737226277372263, 'mean_word_length': 4.848, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 9, 'https://': 0, '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': '2577943', 'n_tokens_mistral': 870, 'n_tokens_neox': 817, 'n_words': 213}