Missing joint_binary_counter module

[GoogleCodeExporter]

What steps will reproduce the problem?
1. Attempt to run python jsm.py with any set of parameters.
2.
3.

What is the expected output? What do you see instead?

Traceback (most recent call last):
 File "jsm.py", line 9, in <module>
   from joint_snv_mix.runners.train import snv_mix_one_train, snv_mix_two_train, joint_snv_mix_one_train, \
 File "/Users/dgoode/Downloads/JointSNVMix-0.7.5/joint_snv_mix/runners/train.py", line 8, in <module>
   from joint_snv_mix.counters.joint_binary_counter import JointBinaryBaseCounter
ImportError: No module named joint_binary_counter

What version of the product are you using? On what operating system?

SNVmix 0.7.5 on Mac OS 10.7 (Lion)

Please provide any additional information below.

Installed JointSNVmix on a Mac this time, but having problems getting it to 
run. I installed Cython and pysam 0.5 prior to installing JointSNVmix.

Original issue reported on code.google.com by dgoode.s...@gmail.com on 19 Mar 2012 at 12:02

[GoogleCodeExporter]

Hi,
This looks like the software is not installed properly. Normally the files 
should be put in a folder ending with python/site-packages/joint_snv_mix, this 
looks like it is running from the folder where you unzipped the software.

1) Did you install with `python setup.py install`?
2) If yes to the first are you running jsm.py from inside the folder where you 
unzipped from? If so try changing to any other folder and just running jsm.py.

Hope that helps.

Cheers,
Andy

Original comment by AndrewJL...@gmail.com on 21 Mar 2012 at 3:22

[GoogleCodeExporter]

Hi Andy,

I did install with `python setup.py install`, but I didn't have permission to 
write to /Library/Python/. I got someone with root access to do the install and 
now things work fine.

Thanks!

David

Original comment by dgoode.s...@gmail.com on 30 Mar 2012 at 2:45

[GoogleCodeExporter]

Original comment by AndrewJL...@gmail.com on 21 Jun 2012 at 9:07

• Changed state: Done

[GoogleCodeExporter]

Hi all,

I've stumbled upon the same problem. After `python setup.py install` I get a 
jsm.py script in the JointSNVMix-0.7.5 directory, and this script keeps 
producing the error that David mentioned. However, if you go to 
JointSNVMix-0.7.5/build/scripts-2.6, you'll find another `jsm.py` that works 
perfectly fine (at least in my case).

Hope this helps.

Irina

Original comment by pulyakh...@gmail.com on 26 Aug 2013 at 1:51

[GoogleCodeExporter]

There seems to be two issues in this thread.

1) After you run `python setup.py install` the file `jsm.py` should be 
installed in your system PATH. This means you should be able to type `jsm.py` 
from any folder in the system and it will work. 

The one exception is if you execute `jsm.py` from the JointSNVMix-0.7.5/ folder 
created during installation. In this case Python get confused because it looks 
at the joint_snv_mix/ folder there instead of the one created during 
installation. This causes problems because certain C extensions aren't compiled 
in that folder. The solution is to exit the JointSNVMix-0.7.5/ folder and run 
`jsm.py`. In Irina's case this worked because she went to the sub-folder 
build/scripts-2.6.

2) The other issue David hit was related to installation permissions. This 
occurs if you are using the system Python installation and don't have root 
privileges. There are two solutions: 1) Get root/administrative permission and 
install. 2) My preferred solution is to create a local Python installation for 
yourself. There is lots of documentation online on howto do this.

Cheers,
Andy 

Original comment by AndrewJL...@gmail.com on 26 Aug 2013 at 6:34