Ambry Databundles

Install

See http://docs.ambry.io for the general documentation, http://docs.ambry.io/en/latest/install_config/install.html for instgallation, and http://docs.ambry.io/en/latest/install_config/configuration.html for additional configuration.

Setup with Miniconda on Mac

You can setup Ambry as a normal package, but the geographic library, GDAL, is really difficult to install, so your Ambry installation won't produce geo databases. The best way to get GDAL installed is with Anaconda.

First, install miniconda, (python 2.7)

.. code-block:: bash

$ wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
$ bash miniconda.sh -b

# Activate the anaconda environment
$ export PATH=~/miniconda/bin:$PATH

Now you can create the environment.

.. code-block:: bash

$ conda create -n ambry python

# Where did conda put it?
$ conda info -e

# Now, activate it.
$ source activate ambry

More about creating conda virtual environments: http://conda.pydata.org/docs/faq.html#env-creating

After setting up anmry, you can use conda to install gdal

.. code-block:: bash

$ git clone https://github.com/<githubid>/ambry.git
$ cd ambry
$ pip install -r requirements.txt
$ conda install gdal
$ python setup.py devel

Postgres extensions notes (Note: If you use virtualenv see DEVEL-README.md)

Full text search

Datasets search implemented on top of PostgreSQL requires postgresql-contrib package and pg_trgm extension.

1. Install postgresql-contrib package.

.. code-block:: bash

    sudo apt-get install postgresql-contrib

2. Install pg_trgm extension:

.. code-block:: bash

    # Switch to postgres user
    $ sudo su - postgres

    # Create schema for ambry library.
    $ psql <db_name> -c 'CREATE SCHEMA IF NOT EXISTS ambrylib;'

    # Grant all privileges on ambrylib schema to ambry user. Assume database user is ambry.
    # psql <db_name> -c 'GRANT ALL PRIVILEGES ON SCHEMA ambrylib to ambry;'

    # Create extension
    $ psql <db_name> -c 'CREATE EXTENSION pg_trgm SCHEMA ambrylib;'

Foreign Data Wrapper (need to query partition files packed with msgpack (mpr files).)

1. Install multicorn:

.. code-block:: bash

wget https://github.com/Kozea/Multicorn/archive/v1.2.3.zip
unzip v1.2.3.zip
cd Multicorn-1.2.3
make && sudo make install

2. Install ambryfdw:

.. code-block:: bash

pip install ambry_sources[geo,fdw]

CKAN export

1. Add CKAN credentials to ~/.ambry-accounts.yaml:

.. code-block:: yaml

ckan:
    host: http://demo.ckan.org        
    organization: <your organization>        
    apikey: <your API key>

2. Run:

.. code-block:: bash

ambry ckan_export <dataset_vid>