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

# Install conda packages
export PATH="$HOME/miniconda3_$TRAVIS_OS_NAME/bin:$PATH"
conda config --add channels conda-forge
conda config --add channels defaults
conda config --add channels r
conda config --add channels bioconda
conda install --yes \
    abyss \
    biopython \
    bedtools \
    pandas \
    networkx
conda clean --all --yes

pushd $HOME
# SDSL-lite
# https://hub.docker.com/r/adamnovak/sequence-graphs/~/dockerfile/
if [[ ! -d $HOME/opt/sdsl-lite ]]; then
    git clone https://github.com/simongog/sdsl-lite.git
fi
pushd $HOME/opt/sdsl-lite && \
sudo ./install.sh /usr/local && \
popd

# biobloomtools
# as in https://github.com/bcgsc/biobloom
if [[ ! -d $HOME/opt/biobloom ]]; then
    git clone https://github.com/bcgsc/biobloom.git
fi
pushd $HOME/opt/biobloom/ && \
git submodule update --init && \
./autogen.sh && \
./configure --prefix=/usr/local && \
make -j 2 && \
sudo make install && \
popd
<commit_msg>Bugfix<commit_after>#!/usr/bin/env bash

# Install conda packages
export PATH="$HOME/miniconda3_$TRAVIS_OS_NAME/bin:$PATH"
conda config --add channels conda-forge
conda config --add channels defaults
conda config --add channels r
conda config --add channels bioconda
conda install --yes \
    abyss \
    biopython \
    bedtools \
    pandas \
    networkx
conda clean --all --yes

pushd $HOME/opt/

# SDSL-lite
# https://hub.docker.com/r/adamnovak/sequence-graphs/~/dockerfile/
if [[ ! -d $HOME/opt/sdsl-lite/ ]]; then
    git clone https://github.com/simongog/sdsl-lite.git
fi
pushd $HOME/opt/sdsl-lite/ && \
sudo ./install.sh /usr/local/ && \
popd

# biobloomtools
# as in https://github.com/bcgsc/biobloom
if [[ ! -d $HOME/opt/biobloom/ ]]; then
    git clone https://github.com/bcgsc/biobloom.git
fi
pushd $HOME/opt/biobloom/ && \
git submodule update --init && \
./autogen.sh && \
./configure --prefix=/usr/local/ && \
make -j 2 && \
sudo make install && \
popd

popd

{'fraction_non_alphanumeric': 0.15721649484536082, 'fraction_numerical': 0.002061855670103093, 'mean_word_length': 2.9371196754563895, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, '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': '3068017', 'n_tokens_mistral': 764, 'n_tokens_neox': 732, 'n_words': 171}