[Bio-linux-dev] Problem with "mothur" in Bio-Linux 6

[Tony Travis]

Hi, Tim.

My colleague Rustam had a problem running "mothur" under Bio-Linux 6 
recently. I had to kludge it to get it working because "uchime" was 
missing and paths appear to be hard-coded in the "mothur" binary:

>[...]
>> In the meantime, was trying to use chimera.slayer and chimera.uchime in
>> Mothur but getting the error messages
>>
>> [ERROR]: /usr/bin/uchime file does not exist. mothur requires the uchime
>> executable.
>> [ERROR]: did not complete chimera.uchime.
>
> Hello, Rustam.
>
> I've installed "uchime" and created symbolic links on bobcat/topcat:
>
>   /usr/bin/uchime -> /usr/local/bin/uchime
>
> It seems that the paths are hard-coded in the "uchime" binary :-(
>
>> [ERROR]: /usr/bin/blast/bin/formatdb file does not exist. mothur
>> requires formatdb.exe.
>> [ERROR]: /usr/bin/blast/bin/blastall file does not exist. mothur
>> requires blastall.exe.
>> [ERROR]: /usr/bin/blast/bin/megablast file does not exist. mothur
>> requires megablast.exe.
>>
>> If anything can be done about this? I do not have access to these
>> directories to check.
>
> OK, I've kludged it so it will now work on bobcat/topcat:
>
>   /usr/bin/blast/bin -> /usr/bin

Can you tell me if any environment variables should be set to allow 
"mothur" to use the conventional Bio-Linux 6 compatible paths?

I installed a separate version of "mothur" from source for QIIME.

Thanks,

   Tony.