[Bioperl-l] Re peatMasker not found

nisa_dar vdar at yorku.ca
Thu May 22 13:54:12 EDT 2008


I am trying to find RepeatMasker program executable by typing 
which RepeatMasker 
but its no where on my system, although I installed it and in my previous
message I have mentioned the paths of its .pm file and its directory. 
I don't know how to find the path of what my program needs, bcs I have tried
all these paths which i mentioned in my previous message.
any suggestions?

 

Florent Angly wrote:
> 
> The path that you set up for $ENV{REPEATMASKERDIR} should be the path to 
> the RepeatMasker program executable, not the path to the ReapeatMasker 
> BioPerl module.
> Florent
> 
> 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?
>>
>>
>>
>>
>> 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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> 

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