[Bioperl-l] Re peatMasker not found

Sendu Bala bix at sendu.me.uk
Thu May 22 13:51:38 EDT 2008


nisa_dar wrote:
> please see my full message and all the approaches that i have been doing to
> tell my pogram where repeat masker is...what else is correct if these are
> not?

We don't know where you installed RepeatMasker. Only you do. You need to 
supply that installation directory to $ENV{REPEATMASKERDIR} in your code.


> Sendu Bala-2 wrote:
>> nisa_dar wrote:
>>> ok now I have installed repeat masker, with its prerequisites as given on 
>>> http://www.repeatmasker.org/
>>> but now I am getting this error message. 
>>>
>>> RepeatMasker program not found as  or not executable. 
>>>
>>> what should I do?
>> Well now you have to correct your code to tell it where you installed 
>> RepeatMasker:
>>
>>
>>>> On May 13, 2008, at 1:59 PM, nisa_dar wrote:
>> [...]
>>>>> BEGIN {
>>>>>
>>>>> 	$ENV{REPEATMASKERDIR} =
>>>>> '/opt/rocks/lib/perl5/site_perl/5.8.8/Bio/Tools/';
>>>>>
>>>>>  }
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>>
>>
> 



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