[Bioperl-l] Re peatMasker not found

[Thomas Sharpton]

'which repeatmasker' can only find executables that are part of your 
system path  (which you can set in your .bashrc file).

Did you follow these instructions when installing?

http://www.repeatmasker.org/RMDownload.html

If so, I'd venture a guess that the RepeatMasker executable is sitting 
in /usr/local/bin or /usr/local/RepeatMasker.

Good luck,

-T

nisa_dar wrote:
> 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 revious
> 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/';
>>>>>>>
>>>>>>>  }
>>>>>>>           
>>>>>>>               
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>>     
>>>>         
>>>   
>>>       
>> _______________________________________________
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>>
>>
>>     
>
>   


-- 
Thomas Sharpton
PhD Candidate - UC Berkeley
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