[Bioperl-l] Re peatMasker not found

nisa_dar vdar at yorku.ca
Thu May 22 14:59:32 EDT 2008


I can see that RepeatMasker program is there in this directory
/home/vdar/RepeatMasker

Here is a whole list of whats inside this directory

[vdar at capsella RepeatMasker]$ ls -al
total 35048
drwxr-xr-x   5 vdar users     4096 May 22 11:41 .
drwx------  10 vdar users     4096 May 22 14:15 ..
-rwxr-xr-x   1 vdar users    11386 May 20 14:26 ArrayListIterator.pm
-rwxr-xr-x   1 vdar users    13888 May 20 14:26 ArrayList.pm
-rw-r--r--   1 vdar users     1683 May 20 14:26 bluegrad.jpg
-rwxr-xr-x   1 vdar users    16439 May 20 14:26 configure
-rwxr-xr-x   1 vdar users    26098 May 20 14:26 CrossmatchSearchEngine.pm
-rwxr-xr-x   1 vdar users    26342 May 20 14:26 DateRepeats
-rw-r--r--   1 vdar users     5935 May 20 14:26 daterepeats.help
-rwxr-xr-x   1 vdar users    33871 May 20 14:26 DeCypherSearchEngine.pm
-rwxr-xr-x   1 vdar users    33265 May 20 14:26 DupMasker
-rwxr-xr-x   1 vdar users    54550 May 20 14:26 FastaDB.pm
-rw-r--r--   1 vdar users     6966 May 20 14:26 HTMLAnnotHeader.html
-rwxr--r--   1 vdar users     2543 May 20 14:26 INSTALL
drwxr-xr-x   2 vdar users     4096 May 20 14:26 Libraries
-rw-r--r--   1 vdar users     9862 May 20 14:26 license.txt
-rwxr-xr-x   1 vdar users   425419 May 20 14:26 LineHash.pm
drwxr-xr-x   4 vdar users     4096 May 20 14:26 Matrices
-rwxr-xr-x   1 vdar users   322391 May 20 14:26 ProcessRepeats
-rwxr-xr-x   1 vdar users     9381 May 20 14:26 PubRef.pm
-rwxr--r--   1 vdar users     1836 May 20 14:26 README
-rwxr-xr-x   1 vdar users    22385 May 20 14:26 RepbaseEMBL.pm
-rwxr-xr-x   1 vdar users    49282 May 20 14:26 RepbaseRecord.pm
-rwxr-xr-x   1 vdar users  3929708 May 20 14:26 RepeatAnnotationData.pm
-rwxr-xr-x   1 vdar users   213727 May 20 14:26 RepeatMasker
-rw-r--r--   1 vdar users     5721 May 20 14:26 RepeatMaskerConfig.pm
-rwxr-xr-x   1 vdar users     5689 May 20 14:26 RepeatMaskerConfig.tmpl
-rw-r--r--   1 vdar users    85557 May 20 14:26 repeatmasker.help
-rwxr-xr-x   1 vdar users    19538 May 20 14:26 RepeatProteinMask
-rwxr-xr-x   1 vdar users    17666 May 20 14:26 SearchEngineI.pm
-rwxr-xr-x   1 vdar users    24600 May 20 14:26 SearchResultCollection.pm
-rwxr-xr-x   1 vdar users    35040 May 20 14:26 SearchResult.pm
-rwxr-xr-x   1 vdar users    11565 May 20 14:26 SeqDBI.pm
-rwxr-xr-x   1 vdar users    25427 May 20 14:26 SimpleBatcher.pm
-rwxr--r--   1 vdar users 30140103 May 20 14:26 taxonomy.dat
-rwxr-xr-x   1 vdar users    23897 May 20 14:26 Taxonomy.pm
-rwxr-xr-x   1 vdar users    20151 May 20 14:26 TRF.pm
-rwxr-xr-x   1 vdar users    14587 May 20 14:26 TRFResult.pm
drwxr-xr-x   2 vdar users     4096 May 20 14:26 util
-rwxr-xr-x   1 vdar users    41181 May 20 14:26 WUBlastSearchEngine.pm
-rwxr-xr-x   1 vdar users    35404 May 20 14:26 WUBlastXSearchEngine.pm
[vdar at capsella RepeatMasker]$ pwd
/home/vdar/RepeatMasker


But when I enter this path in my program like this

BEGIN {

        $ENV{REPEATMASKERDIR} = '/home/vdar/RepeatMasker';

 }

It gives the same error.

Thanks!





Mauricio Herrera Cuadra-3 wrote:
> 
> Sendu already pointed it out: $ENV{REPEATMASKER} needs to be changed. 
> RepeatMasker docs must have some info on where it was installed 
> depending on your platform, use `which` otherwise.
> 
> Mauricio.
> 
> 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
>>>
>>>
>> 
> 
> -- 
> MAURICIO HERRERA CUADRA
> arareko at campus.iztacala.unam.mx
> Laboratorio de Genética
> Unidad de Morfofisiología y Función
> Facultad de Estudios Superiores Iztacala, UNAM
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 

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