__main__.py upon cloning does not work

[TrentBrick]

Thank you so much for making this package!

I am trying to get it working by cloning the repo and calling python __main__.py however, I am running into a lot of issues with dependencies.

1. I had to clone PeptideBuilder from github
2. I had an error with h5py and had to install this and restart my terminal
3. I am now having errors with:

For padding the packed sequences:
Traceback (most recent call last): File "__main__.py", line 165, in <module> train_model_path = train_model("TRAIN", training_file, validation_file, args.learning_rate, args.minibatch_size) File "__main__.py", line 97, in train_model loss = model.compute_loss(primary_sequence, tertiary_positions) File "C:\Users\fmsft\openprotein\openprotein.py", line 41, in compute_loss emissions, backbone_atoms_padded, batch_sizes = self._get_network_emissions(original_aa_string) File "C:\Users\fmsft\openprotein\models.py", line 46, in _get_network_emissions packed_input_sequences = self.embed(original_aa_string) File "C:\Users\fmsft\openprotein\openprotein.py", line 24, in embed torch.nn.utils.rnn.pack_sequence(original_aa_string)) File "D:\Anaconda2\envs\py36\lib\site-packages\torch\nn\utils\rnn.py", line 277, in pack_sequence return pack_padded_sequence(pad_sequence(sequences), [v.size(0) for v in sequences]) File "D:\Anaconda2\envs\py36\lib\site-packages\torch\nn\utils\rnn.py", line 148, in pack_padded_sequence return PackedSequence(torch._C._VariableFunctions._pack_padded_sequence(input, lengths, batch_first)) RuntimeError: Length of all samples has to be greater than 0, but found an element in 'lengths' that is <= 0

And with starting the web server:
self.run() File "C:\Users\fmsft\openprotein\dashboard.py", line 45, in run call(["/bin/bash", "start_web_app.sh"]) File "D:\Anaconda2\envs\py36\lib\subprocess.py", line 267, in call with Popen(*popenargs, **kwargs) as p: File "D:\Anaconda2\envs\py36\lib\subprocess.py", line 709, in __init__ restore_signals, start_new_session) File "D:\Anaconda2\envs\py36\lib\subprocess.py", line 997, in _execute_child startupinfo) FileNotFoundError: [WinError 2] The system cannot find the file specified

[TrentBrick]

I switched over to my Linux subsystem. Still had to install the first 2 dependencies ( PeptideBuilder and h5py) also have to now install npm. These dependencies should be listed out. The code now and the webserver works.

[JeppeHallgren]

Thanks for filing this @TrentBrick - I've added #14 to track the dependency list issue and will close this for now. Let me know if you hit other install issues!

[TrentBrick]

I had to switch back over to windows. I have the code running but can't get the Flask server to work (I know almost nothing about Flask). When I run it I get this error:

File "D:\Anaconda2\envs\py36\lib\threading.py", line 916, in _bootstrap_inner self.run() File "c:\Users\fmsft\PAE-New\dashboard.py", line 45, in run call(["/bin/bash", "start_web_app.sh"]) File "D:\Anaconda2\envs\py36\lib\subprocess.py", line 267, in call with Popen(*popenargs, **kwargs) as p: File "D:\Anaconda2\envs\py36\lib\subprocess.py", line 709, in __init__ restore_signals, start_new_session) File "D:\Anaconda2\envs\py36\lib\subprocess.py", line 997, in _execute_child startupinfo) FileNotFoundError: [WinError 2] The system cannot find the file specified

What edit can I make so that this works on Windows? Thank you.