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# # Installation
#
# The following notebook shows how to install the necessary dependencies to run the analysis [Sex-related differences in the human microbiome using curatedMetagenomicData 3 and the Python 3 language](curatedMetagenomicData%203%20Terminal%20interface,%20sex-contrast%20microbiome%20meta-analysis.ipynb). You must have R (>= 4.1) installed.
#
# ## Install BiocManager and curatedMetagenomicDataTerminal

# + language="bash"
#
# Rscript -e "utils::install.packages('BiocManager', repos = 'http://cran.us.r-project.org')"
# Rscript -e "BiocManager::install('waldronlab/curatedMetagenomicDataTerminal')"
# Rscript -e "curatedMetagenomicDataTerminal::install()"
# -

# If everything went fine, you now should be able to run `curatedMetagenomicData -h`:

# + language="bash"
#
# curatedMetagenomicData -h
# -

# ## Install Python Libraries

# + language="bash"
#
# apt-get install python3-skbio python-skbio-doc
#
# python3 -m pip install pandas \
#   setuptools \
#   numpy \
#   python-dateutil \
#   pytz \
#   statsmodels \
#   matplotlib \
#   seaborn \
#   num2words
# -

# ## Clone the Repository
#
# If you haven't done it already, clone the curatedMetagenomicAnalyses repository. 

# + language="bash"
#
# git clone <EMAIL>:waldronlab/curatedMetagenomicAnalyses.git
# -

# Now you're ready to run [Sex-related differences in the human microbiome using curatedMetagenomicData 3 and the Python 3 language](curatedMetagenomicData%203%20Terminal%20interface,%20sex-contrast%20microbiome%20meta-analysis.ipynb).

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