Source installation instructions not working

[jackwadden]

Describe the bug Source installation instructions and example script do not run to completion on Ubuntu 16.04 LTS

To Reproduce To install Chiron and run the example script, I'm following the steps below from the README (and some supplements). Once I think I have Chiron installed correctly, I'm running using the exact example command from the README (i.e. python chiron/entry.py call -i chiron/example_folder/ -o -m chiron/model/DNA_default -b 1100 -l 400 -j 40 --beam 30 --mode dna)

1. git clone https://github.com/haotianteng/Chiron
2. export PYTHONPATH=:$PYTHONPATH
3. pip install -r requirements.txt (run command; complains about no module named packaging)
4. pip install packaging (run command; complains about no module Bio)
5. pip install biopython (run command; compains about numpy installation being corrupted) 6 pip install -r requirements.txt (run command; runs, but eventually fails)

Chiron then runs but eventually fails with the following error:

Traceback (most recent call last): File "chiron/entry.py", line 154, in main() File "chiron/entry.py", line 146, in main args.func(args) File "chiron/entry.py", line 40, in evaluation chiron_eval.run(args) File "/home/jack/r/Chiron/chiron/chiron_eval.py", line 514, in run Exception in thread Thread-6: Traceback (most recent call last): File "/usr/lib/python2.7/threading.py", line 801, in __bootstrap_inner self.run() File "/usr/lib/python2.7/threading.py", line 754, in run self.target(*self.args, *self.__kwargs) File "/home/jack/.local/lib/python2.7/site-packages/tensorflow/python/training/queue_runner_impl.py", line 250, in _run coord.request_stop(e) File "/home/jack/.local/lib/python2.7/site-packages/tensorflow/python/training/coordinator.py", line 211, in request_stop six.reraise(sys.exc_info()) File "/home/jack/.local/lib/python2.7/site-packages/tensorflow/python/training/queue_runner_impl.py", line 234, in _run sess.run(enqueue_op) File "/home/jack/.local/lib/python2.7/site-packages/tensorflow/python/client/session.py", line 767, in run run_metadata_ptr) File "/home/jack/.local/lib/python2.7/site-packages/tensorflow/python/client/session.py", line 965, in _run feed_dict_string, options, run_metadata) File "/home/jack/.local/lib/python2.7/site-packages/tensorflow/python/client/session.py", line 1015, in _do_run target_list, options, run_metadata) File "/home/jack/.local/lib/python2.7/site-packages/tensorflow/python/client/session.py", line 1035, in _do_call raise type(e)(node_def, op, message) CancelledError: Dequeue operation was cancelled [[Node: fifo_queue_Dequeue = QueueDequeueV2component_types=[DT_FLOAT, DT_STRING, DT_INT32, DT_INT32], timeout_ms=-1, _device="/job:localhost/replica:0/task:0/cpu:0"]]

Environment (please complete the following information):

• OS: Ubuntu 16.04
• Python: 2.7.12

Am I doing anything wrong? If not, could someone sanity check installation from source and help me get the examples running?

Thanks in advance!

-Jack

[haotianteng]

Hi Jack, Please do the following:

git clone https://github.com/haotianteng/Chiron.git
cd Chiron
python setup.py install

Then you can choose to install Tensorflow, or Tensorflow-gpu I have updated the README, thanks for point this out.

[haotianteng]

Okay, so it seems there is some issue with python 2.7 I will try to fix it, but if it's possible you can use python 3.6. Thanks

[haotianteng]

Alright, so it's the threading function in Python 2.7 with Tensorflow causing the problem, I rewrite them into a class and now it's working fine in both Python 2.7 and 3.6, other versions should also be fine. So now it should be fine to install the dependency by

pip install -r requirement.txt

or

python setup.py install