Re: install error

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Chris Miller

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May 31, 2013, 1:24:21 AM5/31/13
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Rick,

Sorry you are having trouble.  How did you download the EMIRGE source?  This file is distributed in the pykseq folder that comes with the ZIP or a git clone.

Is anyone else out there having this problem?
Chris

On Thursday, May 30, 2013 11:16:58 PM UTC-6, Rick White wrote:
python setup.py build
python setup.py install

Then I get this error..
error: /home/rawiii/Programs/EMIRGE/
pykseq/pykseq.pyx: No such file or directory

anna.d...@gmail.com

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Aug 16, 2013, 3:37:11 PM8/16/13
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Hi all!

I am having troubles with running actual emirge.py.
This is what I got:
$ python emirge.py --help
  File "emirge.py", line 4
    <!DOCTYPE html>
    ^
SyntaxError: invalid syntax

Any ideas what could have happened?

anna.d...@gmail.com

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Aug 16, 2013, 4:12:19 PM8/16/13
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Ok, I am having troubles with running emirge.py:
$ python emirge.py --help
Traceback (most recent call last):
  File "emirge.py", line 54, in <module>
    import pysam
  File "/home/annet/Programs/EMIRGE/pysam-0.7.5/pysam/__init__.py", line 1, in <module>
    from pysam.csamtools import *
ImportError: No module named csamtools

What can be the problem?


bleeke...@gmail.com

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Sep 17, 2013, 3:44:57 AM9/17/13
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It looks like you may not have cython installed.  Either way - there is a bug in the pysam modules that has been fixed - although 0.7.5 did not present the issue for me, but I compiled from pip directly after cython was installed.  Here is a link to the pysam user group discussing this typo/bug.

Beatr...@lbl.gov

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Jul 11, 2017, 6:18:38 PM7/11/17
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Hi!! did you get to fix this problem?

Chris Miller

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Jul 12, 2017, 11:22:08 PM7/12/17
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Hi, 

What version of pysam are you using? 

Chris 

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Beatrice Garcia Rodriguez

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Jul 13, 2017, 7:54:50 PM7/13/17
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Hi! Fixed the problem! I had the wrong python version. Thanks for your response.

Beatrice
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Chris Miller

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Jul 17, 2017, 4:08:53 PM7/17/17
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Good to hear it is fixed.  Thanks for reporting back.


On Thursday, July 13, 2017 at 5:54:50 PM UTC-6, Beatrice Garcia Rodriguez wrote:
Hi! Fixed the problem! I had the wrong python version. Thanks for your response.

Beatrice
On Jul 12, 2017, at 8:22 PM, Chris Miller wrote:

Hi, 

What version of pysam are you using? 

Chris 
On Jul 11, 2017 3:18 PM,  wrote:
Hi!! did you get to fix this problem?


On Friday, August 16, 2013 at 12:37:11 PM UTC-7, Anna Doloman wrote:
Hi all!

I am having troubles with running actual emirge.py.
This is what I got:
$ python emirge.py --help
  File "emirge.py", line 4
    <!DOCTYPE html>
    ^
SyntaxError: invalid syntax

Any ideas what could have happened?


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EMIRGE code:
https://github.com/csmiller/EMIRGE

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