[Bioperl-l] Re peatMasker not found

Thomas Sharpton sharpton at berkeley.edu
Thu May 22 14:39:04 EDT 2008


'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
>>>>
>>>>
>>>>     
>>>>         
>>>   
>>>       
>> _______________________________________________
>> Bioperl-l mailing list
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>>
>>
>>     
>
>   


-- 
Thomas Sharpton
PhD Candidate - UC Berkeley
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