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refer to BioThings demo AMI
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sirloon committed Nov 29, 2017
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33 changes: 21 additions & 12 deletions docs/doc/standalone.rst
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Expand Up @@ -19,7 +19,7 @@ Quick Links
If you already know how to run a BioThings standalone instance, you can download the latest
avaiable Docker images from the following tables.

.. note:: images don't contain data but are ready to download and maintain data up-to-date
.. note:: Images don't contain data but are ready to download and maintain data up-to-date
running simple commands through the hub.

|mygenelogo| mygene.info
Expand Down Expand Up @@ -73,8 +73,14 @@ Prerequisites

Using standalone instances requires to have a Docker server up and running, some basic knowledge
about commands to run and use containers. Images have been tested on Docker >=17. Using AWS cloud,
you can use AMI ``ami-6e1a0117`` and install Docker with ``sudo apt-get install docker.io``. You may
need to point Docker images directory to a specific hard drive to get enough space, using ``-g`` option:
you can use our public AMI **biothings_demo_docker** (``ami-40e03938``) with Docker pre-configured
and ready for standalone demo instances deployment. We recommend using instance type with at least
8GiB RAM, such as ``t2.large``. AMI comes with an extra 30GiB EBS volume, which should be enough to
deploy any demo instances.

Alternately, you can install your own Docker server (on recent Ubuntu systems, ``sudo apt-get install docker.io``
is usually enough). You may need to point Docker images directory to a specific hard drive to get enough space,
using ``-g`` option:

.. code:: bash
Expand All @@ -83,14 +89,17 @@ need to point Docker images directory to a specific hard drive to get enough spa
# restart to make this change active
sudo service docker restart
Depending on the type of data you want to use, you may need a large amount of disk space (particularly for
production data and old data). Refer to the `Quick Links`_ section for more information.

Demo instances, on the other hand, use very little disk space, as only a small subset of data is available.
Demo instances use very little disk space, as only a small subset of data is available.
For instance, myvariant demo only requires ~10GiB to run with demo data up-to-date, including the whole Linux
system and all other dependencies. Demo instances provide a quick and easy way to setup a running APIs,
without having to deal with some advanced system configurations.

For deployment with production or old data, you may need a large amount of disk space.
Refer to the `Quick Links`_ section for more information. Bigger instance types will also be
required, and even a full cluster architecture deployment. We'll soon provide guidelines and
deployment scripts for this purpose.


*****************
What you'll learn
*****************
Expand Down Expand Up @@ -294,10 +303,10 @@ We're now connected to the hub, inside a python shell where the application is a
when it's necessary to bring the API data to a specific version (not the latest one), are considered more advanced,
and won't be covered in this guide.
.. note:: because the hub console is actually a python interpreter, we call the commands using parenthesis, just like functions
.. note:: Because the hub console is actually a python interpreter, we call the commands using parenthesis, just like functions
or methods. We can also pass arguments when necessary, just like standard python (remember: it **is** python...)
.. note:: after each command is typed, we need to press "enter" to get either its status (still running) or the result
.. note:: After each command is typed, we need to press "enter" to get either its status (still running) or the result
Let's explore some more.
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0 document(s) added, 0 document(s) deleted, 130 document(s) updated
Local version is 20171126, remote is 20171126, we're up-to-date. We can also use ``check()``:
Local version is ``20171126``, remote is ``20171126``, we're up-to-date. We can also use ``check()``:

.. code:: bash
Expand Down Expand Up @@ -540,7 +549,7 @@ they're fully started and ready.
If after ~1 min, you still don't see the hub running, log to user ``biothings`` and check the starting sequence.
.. note:: hub is running in a tmux session, under user ``biothings``
.. note:: Hub is running in a tmux session, under user ``biothings``
.. code:: bash
Expand All @@ -558,7 +567,7 @@ You should see something looking like this above. If not, you should see the act
fix it (not enough disk space, etc...). The hub can be started again using ``python -m biothings.bin.autohub`` from within the application
directory (in our case, ``/home/biothings/mygene.info/src/``)
.. note:: press Control-B then D to dettach the tmux session and let the hub running in background.
.. note:: Press Control-B then D to dettach the tmux session and let the hub running in background.
Logs are available in ``/data/mygene.info/logs/``. You can have a look at:
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