<commit_before>#!/bin/sh
# shellcheck disable=SC2236

# Include bcbio toolkit binaries in PATH, if defined.
# Attempt to locate bcbio installation automatically on supported platforms.

if [ -z "$BCBIO_EXE" ]
then
    if [ ! -z "$HARVARD_O2" ]
    then
        export BCBIO_EXE="/n/app/bcbio/tools/bin/bcbio_nextgen.py"
    elif [ ! -z "$HARVARD_ODYSSEY" ]
    then
        export BCBIO_EXE="/n/regal/hsph_bioinfo/bcbio_nextgen/bin/bcbio_nextgen.py"
    fi
fi
if [ ! -z "$BCBIO_EXE" ]
then
    # Check that path is valid.
    if [ -f "$BCBIO_EXE" ]
    then
        bcbio_bin_dir="$( dirname "$BCBIO_EXE" )"
        export PATH="${bcbio_bin_dir}:${PATH}"
        unset -v PYTHONHOME PYTHONPATH
        unset -v bcbio_bin_dir
    else
        printf "bcbio does not exist at:\n%s\n" "$BCBIO_EXE"
        # Don't exit here as this can cause SSH lockout.
    fi
fi<commit_msg>Improve bcbio detection on Azure<commit_after>#!/bin/sh
# shellcheck disable=SC2236

# Include bcbio toolkit binaries in PATH, if defined.
# Attempt to locate bcbio installation automatically on supported platforms.

if [ -z "$BCBIO_EXE" ]
then
    if [ ! -z "$AZURE" ]
    then
        BCBIO_EXE="/data00/bcbio/tools/bin/bcbio_nextgen.py"
    elif [ ! -z "$HARVARD_O2" ]
    then
        BCBIO_EXE="/n/app/bcbio/tools/bin/bcbio_nextgen.py"
    elif [ ! -z "$HARVARD_ODYSSEY" ]
    then
        BCBIO_EXE="/n/regal/hsph_bioinfo/bcbio_nextgen/bin/bcbio_nextgen.py"
    fi
fi

# Export in PATH if the binary is accessible.
if [ -x "$BCBIO_EXE" ]
then
    export BCBIO_EXE
    unset -v PYTHONHOME PYTHONPATH
    
    bcbio_bin_dir="$( dirname "$BCBIO_EXE" )"
    export PATH="${bcbio_bin_dir}:${PATH}"
    unset -v bcbio_bin_dir
fi
{'fraction_non_alphanumeric': 0.11816578483245149, 'fraction_numerical': 0.007054673721340388, 'mean_word_length': 2.8947368421052633, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, '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': '2194151', 'n_tokens_mistral': 713, 'n_tokens_neox': 673, 'n_words': 153}