Installation issue

[shaman-narayanasamy]

Dear authors,

I am attempting to install Drep on my cluster. However, I am facing some issues.

Here is what I did:

$ git clone https://github.com/MrOlm/drep.git

$ cd drep

$ pip install --user .

It looks like it goes fine:

Unpacking /mnt/gaiagpfs/users/homedirs/snarayanasamy/repositories/drep
  Running setup.py egg_info for package from file:///mnt/gaiagpfs/users/homedirs/snarayanasamy/repositories/drep
    
Installing collected packages: drep
  Running setup.py install for drep
    changing mode of build/scripts-3.3/dRep from 644 to 755
    
    changing mode of /home/users/snarayanasamy/.local/bin/dRep to 755
Successfully installed drep
Cleaning up...

I have python3.3.2 loaded onto my environment. Then I attempt the test:
$ python3 test_suite.py

To get:

Traceback (most recent call last):
  File "tests/test_suite.py", line 14, in <module>
    from drep import argumentParser
  File "/home/users/snarayanasamy/.local/lib/python3.4/site-packages/drep/argumentParser.py", line 17, in <module>
    from drep.controller import Controller
  File "/home/users/snarayanasamy/.local/lib/python3.4/site-packages/drep/controller.py", line 25, in <module>
    from drep.WorkDirectory import WorkDirectory
  File "/home/users/snarayanasamy/.local/lib/python3.4/site-packages/drep/WorkDirectory.py", line 5, in <module>
    import pandas as pd
ImportError: No module named 'pandas'

I also try to call the script directly:
$ bin/dRep

And get this:

Traceback (most recent call last):
  File "bin/dRep", line 19, in <module>
    import drep.argumentParser
  File "/home/users/snarayanasamy/.local/lib/python3.3/site-packages/drep/__init__.py", line 5, in <module>
    from Bio import SeqIO
ImportError: No module named 'Bio'

Is there something I am missing here?

I look forward to your reply.

Cheers,
Shaman

Update

I proceeded to install all the dependencies via pip. These include:
pandas, matplotlib, seaborn.

I then arrive to this error when trying to run the test:

Traceback (most recent call last):
  File "tests/test_suite.py", line 215, in <module>
    test_cluster()
  File "tests/test_suite.py", line 207, in test_cluster
    verifyCluster.run()
  File "tests/test_suite.py", line 147, in run
    self.functional_test_1()
  File "tests/test_suite.py", line 163, in functional_test_1
    controller.parseArguments(args)
  File "/home/users/snarayanasamy/.local/lib/python3.4/site-packages/drep/controller.py", line 143, in parseArguments
    self.cluster_operation(**vars(args))
  File "/home/users/snarayanasamy/.local/lib/python3.4/site-packages/drep/controller.py", line 50, in cluster_operation
    drep.d_cluster.d_cluster_wrapper(kwargs['work_directory'],**kwargs)
  File "/home/users/snarayanasamy/.local/lib/python3.4/site-packages/drep/d_cluster.py", line 284, in d_cluster_wrapper
    Bdb, data_folder, kwargs = parse_arguments(workDirectory, **kwargs)
  File "/home/users/snarayanasamy/.local/lib/python3.4/site-packages/drep/d_cluster.py", line 316, in parse_arguments
    .format(prog))
NameError: name 'prog' is not defined

[MrOlm]

Hi Sharman,

Thank you for your interest in the program, and thank you for contacting me about its issues- I really appreciate it.

I'm glad you were able to find out about the missing dependencies- I just pushed an update that (in addition to fixing the 'prog' problem) will also install those dependencies automatically.

The second error your referring to is a bug in the program- the easiest way to fix it would be to download the new version of 'drep' that I just made, and then running:

pip install . --upgrade

To upgrade the installation. After upgrading you should see 'version 0.3.5' when running the help, as opposed to 'version 0.3.4'

If this doesn't work please let me know.

Thanks again,
-Matt