Project: De novo Peptide Sequencing by Deep Learning.
Author: Hieu Tran (@nh2tran, hieutran1985@gmail.com).
Publication: De novo Peptide Sequencing by Deep Learning. Proceedings of the National Academy of Sciences, 2017.
Data repository: ftp://massive.ucsd.edu/MSV000081382
DeepNovo is implemented and tested with Python 2.7 and TensorFlow r0.10. In addition, DeepNovo also uses Numpy and Cython.
Here we provide instructions for installing Python and TensorFlow on Linux Ubuntu.
Step 1: Install Python 2.7, pip, and virtualenv using the following commands
$ sudo apt-get install python2.7
$ sudo apt-get install python-pip python-dev python-virtualenv
You can then check the version of Python using the following command
$ python --version
Step 2: Install TensorFlow with virtualenv.
Virtualenv is a virtual Python environment isolated from other Python development, incapable of interfering with or being affected by other Python programs on the same machine.
To start working with TensorFlow, you simply need to "activate" the virtual environment.
When you are done using TensorFlow, you may "deactivate" the environment.
Step 2.1: Create a virtualenv environment using the following command
$ virtualenv --system-site-packages ~/tensorflow
Step 2.2: Activate the virtualenv environment using the following command
$ source ~/tensorflow/bin/activate
Step 2.3: Install TensorFlow version r.0.10 using the following command where URL depends on CPU/GPU support
(tensorflow)$ pip install --upgrade URL
# with CPU support only
URL=https://storage.googleapis.com/tensorflow/linux/cpu/tensorflow-0.10.0-cp27-none-linux_x86_64.whl
# with NVIDIA-GPU support
URL=https://storage.googleapis.com/tensorflow/linux/gpu/tensorflow-0.10.0-cp27-none-linux_x86_64.whl
Step 2.4: Check TensorFlow version, installation, device
$ python
>>> import tensorflow as tf
>>> print(tf__version__)
>>> sess = tf.InteractiveSession()
>>> sess.close()
>>> quit()
Step 2.5: Deactivate the virtualenv environment using the following command
(tensorflow)$ deactivate
Step 3: Install Cython using the following command
$ pip install Cython
To use DeepNovo in the TensorFlow enviroment, you need to activate/deactivate the enviroment as mentioned earlier. Further details of DeepNovo usage are provided in the README files in each folder.