JointSNVMix installation in Arch linux

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What steps will reproduce the problem?
1.Installing JointSNVMix-0.7.5 and JoinSNVMix-0.8-b2

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

Expected output is proper installation and able to run jsm.py. However, when I 
try to install JointSNVMix-0.7.5, I get the following error: command 'gcc' 
failed with exit status 1. This seems to be the problem associated with python 
development headers, but it should be installed.

When installing JointSNVMix-0.8-b2, there seems to be some sort of syntax 
errors occurring and I get the following SyntaxError: invalid syntax. I do get 
jsm.py installed in my path, but when I run jsm.py train -h, I get the 
following RuntimeError: maximum recursion depth exceeded in comparison, and no 
list of option is generated.

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

I tried both JoinSNVMix-0.7.5 and JointSNVMix-0.8-b2. I believe I have all the 
dependencies installed properly, but please let me know if the problem seems to 
be coming from them. I'm using Arch Linux at the moment, but I remember getting 
similar errors in Mac OS X, which I gave up trying to install few weeks ago.

Please provide any additional information below.

List of dependencies/version numbers
Python: python-3.3.2-2 (I think this might be the problem.. I'm reading python 
2 and 3 are not compatible... any thoughts?)
Cython: python-cython 0.15.1-2
Pysam: python-pysam 0.7.5-2
Alglib: alglib 3.7.0-1

Thanks!

David

Original issue reported on code.google.com by DavidK...@gmail.com on 12 Nov 2013 at 7:33

[GoogleCodeExporter]

Hi David,
I think you are right, Python 3 is the problem. Try using the latest version of 
Python 2. Python 3 changes syntax and JointSNVMix was written for Python 2.

Let me know if that fixes it.

Cheers,
Andy

Original comment by AndrewJL...@gmail.com on 12 Nov 2013 at 7:39

[GoogleCodeExporter]

Hi Andy,

Indeed using Python 2 fixed the problem. For anyone interested in the same 
issue, I used $ python2 setup.py install, which may not be relevant in other OS 
and changed the first line in jsm.py from #!/usr/bin/python to 
#!/usr/bin/python2 However, now I'm getting the following ImportError: No 
module named csamtools. This seems to be a problem with pysam. I'm not entirely 
sure, but I suspect this is also python 2 and 3 incompatibility issue. I'm 
currently trying to see how I can work this around, but if you have any input 
to this please let me know.

Thanks!

David

Original comment by DavidK...@gmail.com on 12 Nov 2013 at 12:55

[GoogleCodeExporter]

Hi David,
If you are using version 0.7.5 you will need to install Pysam 0.5.0, not a 
newer version. If you are using 0.8.0 it shouldn't be an issue since I stopped 
linking against the library.

Cheers,
Andy

Original comment by AndrewJL...@gmail.com on 12 Nov 2013 at 6:27

[GoogleCodeExporter]

Hi Andy,

What I ended up doing was to completely re-install 0.8-b2, and now I'm getting 
different ImportError: No module named xalglib.

Now I've looked through and found that someone already had the same problem. It 
turns out the user simply went back to 0.7.5. However it is strange, since I 
already have alglib 3.7.0-1 properly installed. Do you have any inputs?

Thanks so much for such timely responses.

David

Original comment by DavidK...@gmail.com on 13 Nov 2013 at 4:29

[GoogleCodeExporter]

Hi Derek,
If you open the Python 2 interpreter and type `import xalglib` do you get an 
error?

Also did you run `python2 setup.py` or `python setup.py` to install JoinSNVMix?

Cheers,
Andy

Original comment by AndrewJL...@gmail.com on 13 Nov 2013 at 4:35

[GoogleCodeExporter]

Hi Andy,

When I start up python2 (Python 2.7.5) then type 'import xalglib', I get the 
following error
Tracemabck (most recent call last):
 File "<stdin>", line 1, in <module>
ImportError: No module named xalglib.

I had a suspicion that this maybe due to the fact that I have both python 2 and 
3 installed and alglib is only working in python 3. So I repeated the same 
command in python 3 (Python 3.3.2) and I get the same error. Perhaps the 
library is not properly installed?

Also, I ran $ python2 setup.py install

Thank you again

David

Original comment by DavidK...@gmail.com on 13 Nov 2013 at 4:53

[GoogleCodeExporter]

Just to close up this problem, I was able to install it under Mac OSX. The 
problem was that I didn't follow the proper alglib installation procedure, 
which is found in 
http://www.alglib.net/translator/man/manual.cpython.html#gs_unix_installing

I haven't ran any process with it yet, but jsm.py train -h gives proper help 
output.

Thanks!

david

Original comment by DavidK...@gmail.com on 10 Jan 2014 at 5:03