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Updated MongoDB installation
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John David Lin committed Aug 20, 2018
1 parent 7605ecb commit e163209
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2 changes: 1 addition & 1 deletion docs/Downstream.rst
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Expand Up @@ -55,7 +55,7 @@ As long as you have a MongoDB instance running and an annotation job ran success
through `pymongo <https://api.mongodb.com/python/current/>`_ as shown by the code below.
Running the query will return a :code:`cursor` object, which can be iterated upon.

If instead a list is intended to be created from it, simply add: `filter2 = list(filter2)`
If instead a list is intended to be created from it, simply add: `filter2 = list(filter2)`.

.. WARNING:: If the number of variants in the database is large and the filtering is not set up correctly,
returning a list will be probably crash your computer since lists are kept in memory. Iterating over the cursor
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11 changes: 1 addition & 10 deletions docs/Introduction.rst
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Expand Up @@ -33,18 +33,9 @@ The simplest way to install VAPr is from PyPI_ with pip_, Python's preferred pac
MongoDB
~~~~~~~

Further, MongoDB needs to installed and running. See the `official instructions <https://docs.mongodb.com/manual/installation>`_
for details on how to install it on your platform. Alternatively, using Docker (possibly the easiest way):
VAPr is written in Python and stores variant annotations in NoSQL database, using a locally-installed instance of MongoDB. `Installation instructions <https://docs.mongodb.com/manual/administration/install-community/>`_


.. code-block:: bash
$ docker run --name vapr -it -p 27017:27017 mongo
This may take a few seconds since the mongodb image needs to be downloaded from a repository. The process
should produce logs that tells you that mongodb is running inside the container. Feel free to leave this
terminal window open and proceed with the rest of the installation.

.. _PyPI: https://pypi.python.org/pypi/yellowbrick
.. _pip: https://docs.python.org/3/installing/

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