[miso-users] Miso 0.5.1 installation error

[Yarden Katz]

Hi Nastasja,

How did you install MISO?  You have to use a package manager like easy_install (preferably distribute's version of easy_install) or pip to get the proper binary scripts without the *.py files made.  Otherwise, it will not be able to find "sam_to_bam" which sounds like the error you're getting, where sam_to_bam is misinterpreted as a bash script.  See: http://genes.mit.edu/burgelab/miso/docs/#installing-fastmiso

Can you let me know your exact installation command?

Best, --Yarden
 

On Mar 4, 2014, at 9:10 AM, Nastasja Kreim wrote:

> Hello,
> 
> I tried to install miso 0.5.1 with python 7.7.3  or pyhton 2.6.6 today.
> The check for the availability of modules went fine. There is no bin 
> directory created and there are no python files without the postfix py.
> 
> After making the pythons scripts available I get the following error 
> running test_miso.py:
> 
> Running test_miso.py gives the following error after throwing a syntax 
> error sam_to_bam:
> sam_to_bam: line 8: syntax error near unexpected token `('
> sam_to_bam: line 8: `def sam_to_bam(sam_filename, output_dir,'
> 
> I do have the same issues with the 0.5.0 and the newest git hub version. 
> Version 0.4.9 does work fine.
> Do you have a hint for me what could get wrong here?
> Thanks.
> 
> Regards
> Nastasja
> 
> -- 
> Nastasja Kreim
> Institute for Molecular Biology gGmbH
> Funded by the Boehringer Ingelheim Foundation
> Ackermannweg 4
> 55128 Mainz
> Germany
> Tel: +49(6131) 39 21527
> Mail: n.kreim at imb-mainz.de
> www.imb-mainz.de
> 
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--
Yarden Katz <yarden at mit.edu>