Commit b1739816 authored by Bharath Ramsundar's avatar Bharath Ramsundar Committed by GitHub
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Update README.md

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@@ -12,7 +12,6 @@ Requirements
* [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)
@@ -23,7 +22,7 @@ Requirements
Linux (64-bit) Installation 
---------------------------

```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.
```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.

1. Anaconda 2.7
   Download the **64-bit Python 2.7** version of Anaconda for linux [here](https://www.continuum.io/downloads#_unix).  
@@ -54,42 +53,36 @@ Linux (64-bit) Installation
   conda install joblib 
   ```

7. `theano`
7. `keras`
   ```bash
   conda install -c omnia theano
   pip install keras
   ```

8. `keras`
   ```bash
   conda install -c omnia keras
   ```

9. `six`
8. `six`
   ```bash
   conda install six
   ```
10. `dill`
9. `dill`
    ```bash
    conda install dill
    ```

11. `ipyparallel`
10. `ipyparallel`
    ```bash
    conda install ipyparallel
    ```

12. `mdtraj`
11. `mdtraj`
   ```bash
   conda install -c omnia mdtraj
   ```
   
13. `scikit-learn`
12. `scikit-learn`
    ```bash
    conda install scikit-learn 
    ```


14. `tensorflow`: Installing `tensorflow` on older versions of Linux (which
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:
@@ -97,7 +90,7 @@ Linux (64-bit) Installation
    conda install -c https://conda.anaconda.org/jjhelmus tensorflow
    ```

15. `deepchem`: Clone the `deepchem` github repo:
14. `deepchem`: Clone the `deepchem` github repo:
    ```bash
    git clone https://github.com/deepchem/deepchem.git
    ```
@@ -106,7 +99,7 @@ Linux (64-bit) Installation
    python setup.py install
    ```

16. To run test suite, install `nosetests`:
15. To run test suite, install `nosetests`:
    ```bash
    pip install nose 
    ```
@@ -117,7 +110,9 @@ Linux (64-bit) Installation
    You might need to uninstall a system install of `nosetests` if
    there is a conflict.

17. If installation has been successful, all tests in test suite should pass:
16. If installation has been successful, all tests in test suite should pass:
    ```bash
    nosetests -v deepchem --nologcapture 
    ```
    Note that the full test-suite uses up a fair amount of memory. 
    Try running tests for one submodule at a time if memory proves an issue.