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American-Gut

American Gut open-access code and IPython notebooks

A note about data

American Gut sequences and metadata are deposited in The European Bioinformatics Institute under the accession ERP012803.

Bloom sequences found in the data repository are correct and up to date.

OTU tables and mapping files hosted in this repository reflects the state of the project in May 2015 and before. This includes an earlier version of the American Gut survey and dietary questionnaire. Data in GitHub has been scrubbed for PHI. A listing of processed data with the new survey can be found at ftp://ftp.microbio.me/AmericanGut.

The latest OTU tables and precalculated diversity comparisons generated by the primary processing notebook set can be found at ftp://ftp.microbio.me/AmericanGut/latest.

======= American Gut open-access data and IPython notebooks

INSTALL

Basics

American-Gut repository is intended to be used as a project/repo meaning there is no need to install it (ignore setup.py at the moment).

After cloning the repository and before using the scripts user should install necessary dependencies. Two approaches are supported at the moment.

Conda based

If you're choice of package manager is conda dependencies can be installed with

$ conda install --file ./conda_requirements.txt
$ pip install -r ./pip_requirements.txt

If you would like to install dependencies within a conda environment be sure to change to the appropriate environment prior to the installation of dependencies.

Note: Be aware that with pip some libraries will have to be compiled from source so appropriate system libraries should be installed prior to running the pip command. For more details take a look at Supported Systems section.

PIP based

$ pip install numpy==1.9.2
$ pip install -r ./pip_requirements.txt

If you would like to install dependencies within a virtualenv environment be sure to change to the appropriate environment prior to the installation of dependencies.

Note: Be aware that with pip some libraries will have to be compiled from source so appropriate system libraries should be installed prior to running the pip command. For more details take a look at Supported Systems section.

Supported Operating Systems / Distributions

Debian 8

Tested with Debian 8.3.0 (amd64).

To compile dependencies from source appropriate libraries can be installed (as root/sudo) with

(root/sudo)$ aptitude install pkg-config libxslt1-dev libxml2 libfreetype6 \
    build-essential python-pip python-dev liblapack-dev liblapack3 \
    libfreetype6-dev libblas-dev libblas3 gfortran libhdf5-serial-dev libsm6

RUN

Basics

Although American-Gut repo provides separate scripts (scripts folder) and a package (americangut folder) it is primarily intended to be used through notebooks (ipynb folder).

There are a few environment variable that can be used to customize the run:

  • AG_TESTING: if set to True scripts will not download AmericanGut EBI data (ERP012803) but instead work with test data (subset of the original EBI data). This is useful for testing.
  • AG_CPU_COUNT: Number of process to use when parallelizing code (defaults to the number of cores)

To generate reports (pdfs) a TeX distribution should be installed on the system.

Adjusting environment on POSIX systems

Since American-Gut repo contains scripts and packages we need to adjust PYTHONPATH and PATH to reflect this. Therefore, prior to working with notebooks execute the following from within the American-Gut repo:

REPO=`pwd`
$ export PYTHONPATH=$REPO/:$PYTHONPATH
$ export PATH=$REPO/scripts:$PATH

If needed adjust AG_* environment variables from Basics section.

Run notebooks

Notebooks are written in two formats and therefore require different profiles.

Markdown based notebooks

Markdown based notebooks can be found in ./ipynb/primary-processing/ folder and have extension md. To use these notebooks we first need to create a profile for ag_ipymd with

$ ipython profile create ag_ipymd

and adjust newly created /path/to/.ipython/profile_ag_ipymd/ipython_notebook_config.py by adding

#------------------------
# ipymd
#------------------------
c.NotebookApp.contents_manager_class = 'ipymd.IPymdContentsManager'

to the end of the file.

Now, we can start ipython with

$ ipython notebook --profile=ag_ipymd

and visit the newly started notebook server by going to http://localhost:8888

Jupyter/IPython based notebooks

Notebooks in native notebook format (ipynb) can be found in ./ipynb/ folder and have the extension ipynb. To use these notebooks we first need to create a profile for ag_default with

$ ipython profile create ag_default

Now, we can start ipython with

$ ipython --profile=ag_default notebook

and visit the newly started notebook server by going to http://localhost:8888