<commit_before>before_install:
  - sudo add-apt-repository -y "deb http://archive.ubuntu.com/ubuntu/ trusty main universe"
  - sudo apt-get -qq update

install:
  - sudo apt-get install --yes --force-yes circos build-essential wget fasttree hmmer lua5.1 blast2 ncbi-blast+ unzip cpanminus mummer python-setuptools exonerate snap infernal mafft
  - sudo ln -s /usr/bin/fasttree /usr/bin/FastTree
  - sudo test/travis.setup-augustus.sh > /dev/null
  - sudo test/travis.setup-gt.sh > /dev/null
  - sudo test/travis.setup-last.sh > /dev/null 
  - sudo test/travis.setup-orthomcl.sh > /dev/null
  - sudo test/travis.setup-aragorn.sh > /dev/null
  - sudo test/travis.setup-gff3toembl.sh > /dev/null
  - sudo cpanm -q --force Carp Storable Bio::SearchIO List::Util Getopt::Long
  - curl -fsSL get.nextflow.io | bash
  - wget -q http://geneontology.org/ontology/go.obo
  - wget -q http://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz
  - zcat Pfam-A.hmm.gz | test/split_hmm.lua 1000 > Pfam-A.hmm<commit_msg>fix file name<commit_after>before_install:
  - sudo add-apt-repository -y "deb http://archive.ubuntu.com/ubuntu/ trusty main universe"
  - sudo apt-get -qq update

install:
  - sudo apt-get install --yes --force-yes circos build-essential wget fasttree hmmer lua5.1 blast2 ncbi-blast+ unzip cpanminus mummer python-setuptools exonerate snap infernal mafft
  - sudo ln -s /usr/bin/fasttree /usr/bin/FastTree
  - sudo test/travis.setup-augustus.sh > /dev/null
  - sudo test/travis.setup-gt.sh > /dev/null
  - sudo test/travis.setup-last.sh > /dev/null 
  - sudo test/travis.setup-orthomcl.sh > /dev/null
  - sudo test/travis.setup-aragorn.sh > /dev/null
  - sudo test/travis.setup-gff3toembl.sh > /dev/null
  - sudo cpanm -q --force Carp Storable Bio::SearchIO List::Util Getopt::Long
  - curl -fsSL get.nextflow.io | bash
  - wget -q http://geneontology.org/ontology/go.obo
  - wget -q http://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz
  - zcat Pfam-A.hmm.gz | test/split-hmm.lua 1000 > Pfam-A.hmm
{'fraction_non_alphanumeric': 0.13730314960629922, 'fraction_numerical': 0.007874015748031496, 'mean_word_length': 3.0337301587301586, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 17, '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': '7073855', 'n_tokens_mistral': 851, 'n_tokens_neox': 786, 'n_words': 165}