<commit_before>language: perl
perl:
  - "5.24-shrplib"
dist: xenial
sudo: false # faster builds as long as you don't need sudo access
addons:
  apt:
    sources:
    - boost-latest
    packages:
    - build-essential
    - file
    - git
    - libboost-all-dev
    - libgdbm-dev
    - expat
    - libberkeleydb-perl
    - openssl
    - bioperl
    - curl
    - ruby2.3-dev
    - rubygems
before_install:
  # Perl modules
  - export PERL5LIB=$PERL5LIB:$HOME/lib/perl5
  - cpanm -l ~ Statistics::Descriptive
  - cpanm -l ~ File::Slurp
  - perl -MData::Dumper -MFile::Slurp -MStatistics::Descriptive -Mthreads -e 'print Dumper \%INC'
  # CGP
  - wget --no-check-certificate https://github.com/lskatz/CG-Pipeline/archive/v0.5.tar.gz
  - tar zxvf v0.5.tar.gz
  - export PATH=$PATH:$(pwd -P)/CG-Pipeline-0.5/scripts
  # Homebrew installation
  - export PATH=$PATH:$HOME/.linuxbrew/bin
  - export HOMEBREW_FORCE_VENDOR_RUBY=1
  - git clone https://github.com/Homebrew/brew $HOME/.linuxbrew/Homebrew
  - mkdir $HOME/.linuxbrew/bin
  - ln -s ../Homebrew/bin/brew $HOME/.linuxbrew/bin
  - eval $($HOME/.linuxbrew/bin/brew shellenv)
  - REALLY_GEM_UPDATE_SYSTEM=1 gem update --system
  - gem install activesupport plist backports
  # Screw installing perl and python incorrectly and slowly in brew.
  # Force the system perl and python.
  # PERL
  - mkdir -pv $HOME/.linuxbrew/Cellar/perl/5.28.1/bin
  - ln -sv `which perl` $HOME/.linuxbrew/Cellar/perl/5.28.1/bin
  - brew link perl
  # PYTHON
  - mkdir -p $HOME/.linuxbrew/Cellar/python@2/2.7.15_1/bin
  - ln -sv `which python` $HOME/.linuxbrew/Cellar/python@2/2.7.15_1/bin/
  - brew link python@2
  # WGET
  - mkdir -p $HOME/.linuxbrew/Cellar/wget/1.20.1/bin
  - ln -sv `which wget` $HOME/.linuxbrew/Cellar/wget/1.20.1/bin/
  - brew link wget
install:
  - brew tap brewsci/bio
  - brew install skesa --force-bottle
  - brew install blast --force-bottle
  # mlst prereqs
  - brew install --force-bottle gzip gdbm openssl berkeley-db libbsd expat pkg-config gpatch ncurses gettext libunistring libidn2 readline sqlite util-linux wget
  - brew install mlst
  # prokka prereqs
  - brew install --force-bottle bioperl less aragorn barrnap blast hmmer infernal minced parallel prodigal tbl2asn
  - brew install prokka
  # Kraken
  #- brew install --force-bottle kraken
  #- wget --no-check-certificate https://ccb.jhu.edu/software/kraken/dl/minikraken_20171019_4GB.tgz
  #- tar zxvf minikraken_20171019_4GB.tgz
  # Krona
  #- wget --no-check-certificate https://github.com/marbl/Krona/archive/xl2.5.tar.gz
  #- tar zxvf xl2.5.tar.gz
  #- perl Krona-xl2.5/KronaTools/install.pl -prefix $HOME/krona
  # Configure SneakerNet
  - cp -rv config.bak config
  - sed -i '/KRAKEN_DEFAULT_DB/d' config/settings.conf
  - sed -i '/KRAKENDIR/d' config/settings.conf
  - echo -e "KRAKEN_DEFAULT_DB\t$(pwd -P)/minikraken_20171013_4GB" >> config/settings.conf
  - echo -e "KRAKENDIR\t$HOME/.linuxbrew/bin" >> config/settings.conf
  - sed -i '/KRONADIR/d' config/settings.conf<commit_msg>removed brew install wget from travis<commit_after>language: perl
perl:
  - "5.24-shrplib"
dist: xenial
sudo: false # faster builds as long as you don't need sudo access
addons:
  apt:
    sources:
    - boost-latest
    packages:
    - build-essential
    - file
    - git
    - libboost-all-dev
    - libgdbm-dev
    - expat
    - libberkeleydb-perl
    - openssl
    - bioperl
    - curl
    - ruby2.3-dev
    - rubygems
before_install:
  # Perl modules
  - export PERL5LIB=$PERL5LIB:$HOME/lib/perl5
  - cpanm -l ~ Statistics::Descriptive
  - cpanm -l ~ File::Slurp
  - perl -MData::Dumper -MFile::Slurp -MStatistics::Descriptive -Mthreads -e 'print Dumper \%INC'
  # CGP
  - wget --no-check-certificate https://github.com/lskatz/CG-Pipeline/archive/v0.5.tar.gz
  - tar zxvf v0.5.tar.gz
  - export PATH=$PATH:$(pwd -P)/CG-Pipeline-0.5/scripts
  # Homebrew installation
  - export PATH=$PATH:$HOME/.linuxbrew/bin
  - export HOMEBREW_FORCE_VENDOR_RUBY=1
  - git clone https://github.com/Homebrew/brew $HOME/.linuxbrew/Homebrew
  - mkdir $HOME/.linuxbrew/bin
  - ln -s ../Homebrew/bin/brew $HOME/.linuxbrew/bin
  - eval $($HOME/.linuxbrew/bin/brew shellenv)
  - REALLY_GEM_UPDATE_SYSTEM=1 gem update --system
  - gem install activesupport plist backports
  # Screw installing perl and python incorrectly and slowly in brew.
  # Force the system perl and python.
  # PERL
  - mkdir -pv $HOME/.linuxbrew/Cellar/perl/5.28.1/bin
  - ln -sv `which perl` $HOME/.linuxbrew/Cellar/perl/5.28.1/bin
  - brew link perl
  # PYTHON
  - mkdir -p $HOME/.linuxbrew/Cellar/python@2/2.7.15_1/bin
  - ln -sv `which python` $HOME/.linuxbrew/Cellar/python@2/2.7.15_1/bin/
  - brew link python@2
  # WGET
  - mkdir -p $HOME/.linuxbrew/Cellar/wget/1.20.1/bin
  - ln -sv `which wget` $HOME/.linuxbrew/Cellar/wget/1.20.1/bin/
  - brew link wget
install:
  - brew tap brewsci/bio
  - brew install skesa --force-bottle
  - brew install blast --force-bottle
  # mlst prereqs
  - brew install --force-bottle gzip gdbm openssl berkeley-db libbsd expat pkg-config gpatch ncurses gettext libunistring libidn2 readline sqlite util-linux
  - brew install mlst
  # prokka prereqs
  - brew install --force-bottle bioperl less aragorn barrnap blast hmmer infernal minced parallel prodigal tbl2asn
  - brew install prokka
  # Kraken
  #- brew install --force-bottle kraken
  #- wget --no-check-certificate https://ccb.jhu.edu/software/kraken/dl/minikraken_20171019_4GB.tgz
  #- tar zxvf minikraken_20171019_4GB.tgz
  # Krona
  #- wget --no-check-certificate https://github.com/marbl/Krona/archive/xl2.5.tar.gz
  #- tar zxvf xl2.5.tar.gz
  #- perl Krona-xl2.5/KronaTools/install.pl -prefix $HOME/krona
  # Configure SneakerNet
  - cp -rv config.bak config
  - sed -i '/KRAKEN_DEFAULT_DB/d' config/settings.conf
  - sed -i '/KRAKENDIR/d' config/settings.conf
  - echo -e "KRAKEN_DEFAULT_DB\t$(pwd -P)/minikraken_20171013_4GB" >> config/settings.conf
  - echo -e "KRAKENDIR\t$HOME/.linuxbrew/bin" >> config/settings.conf
  - sed -i '/KRONADIR/d' config/settings.conf
{'fraction_non_alphanumeric': 0.12833692588293816, 'fraction_numerical': 0.02652959708174432, 'mean_word_length': 2.8840952994204767, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 11, 'https://': 8, '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': '43609', 'n_tokens_mistral': 2480, 'n_tokens_neox': 2362, 'n_words': 501}