Merge pull request #205 from rbharath/grabbag

deepchem

=============

Deep Learning Toolchain for Cheminformatics and Protein Analysis

Deep Learning Toolchain for Drug Discovery and Quantum Chemistry

Requirements

------------

* [openbabel](http://openbabel.org/wiki/Main_Page)

* [pandas](http://pandas.pydata.org/)

* [rdkit](http://www.rdkit.org/docs/Install.html)

* [boost](http://www.boost.org/)

* [joblib](https://pypi.python.org/pypi/joblib)

* [sklearn](https://github.com/scikit-learn/scikit-learn.git)

* [numpy](https://store.continuum.io/cshop/anaconda/)

* [theano](http://deeplearning.net/software/theano/)

* [keras](http://keras.io)

* [six](https://pypi.python.org/pypi/six)

* [dill](https://pypi.python.org/pypi/dill)

* [ipyparallel](https://ipyparallel.readthedocs.io/en/latest/)

* [mdtraj](http://mdtraj.org/)

* [tensorflow](https://www.tensorflow.org/)

Linux (64-bit) Installation 

------------------

---------------------------

```deepchem``` currently requires Python 2.7

```deepchem``` currently requires Python 2.7, and is not supported on any platforms except 64 bit linux. Please make sure you follow the directions below precisely. While you may already have system versions of some of these packages, there is no guarantee that `deepchem` will work with alternate versions than those specified below. This is especially true for the `keras` library, where `deepchem` is known not to work with the latest default version.

###Anaconda 2.7

1. Anaconda 2.7

   Download the **64-bit Python 2.7** version of Anaconda for linux [here](https://www.continuum.io/downloads#_unix).  

   Follow the [installation instructions](http://docs.continuum.io/anaconda/install#linux-install)

###openbabel

2. `openbabel`

   ```bash

   conda install -c omnia openbabel

   ``` 

Follow the onscreen installation instructions

3. `pandas`

   ```bash

   conda install pandas 

   ```

###rdkit

4. `rdkit`

   ```bash

   conda install -c omnia rdkit

   ```

Follow the onscreen installation instructions

5. `boost`

   ```bash

   conda install -c omnia boost=1.59.0

   ```

###keras

Clone the keras git repository

6. `joblib`

   ```bash

git clone https://github.com/fchollet/keras.git

   conda install joblib 

   ```

Cd into the keras directory and execute

7. `theano`

   ```bash

python setup.py install

   conda install -c omnia theano

   ```

8. `keras`

   ```bash

   conda install -c omnia keras

   ```

9. `six`

   ```bash

   conda install six

   ```

10. `dill`

    ```bash

    conda install dill

    ```

11. `ipyparallel`

    ```bash

    conda install ipyparallel

    ```

###deepchem

Clone the deep_chem git repository

12. `mdtraj`

   ```bash

git clone https://github.com/pandegroup/deepchem.git

   conda install -c omnia mdtraj

   ```

13. `tensorflow`: Installing `tensorflow` on older versions of Linux (which

    have glibc < 2.17) can be very challenging. For these older Linux versions,

    contact your local sysadmin to work out a custom installation. If your

    version of Linux is recent, then the following command will work:

    ```

    conda install -c https://conda.anaconda.org/jjhelmus tensorflow

    ```

14. `deepchem`: Clone the `deepchem` github repo:

    ```bash

    git clone https://github.com/deepchem/deepchem.git

    ```

    `cd` into the `deepchem` directory and execute

    ```bash

    python setup.py install

    ```

Cd into the deepchem directory and execute 

15. If installation has been successful, all tests in test suite should pass:

    ```bash

python setup.py develop

    nosetests -v deepchem --nologcapture 

    ```