[maker-devel] change the PATH to gmhmm_wrap

[Carson Holt]

You could create the directory maker/bin for the current installation and
move all executables there from the
/xanadu/site/common/VERSIONS/perl-1.7/bin/ directory.  Then run the
executable installed in the maker/bin directory.  MAKER is expecting to go
back one directory to find libraries and scripts in the MAKER base
directory i.e. ../lib/Widget/genemark/gmhmm_wrap

Thanks,
Carson



On 12-07-05 12:55 PM, "Christoph Hahn" <chrisi.hahni at gmail.com> wrote:

>Dear Carson,
>
>Thanks for your reply! I have already requested the installation of
>maker 2.25 from the cluster admin, but unfortunately this will take a
>while. I guess there is no way for me to fix that for the moment in
>maker 2.10??
>
>Thanks again!
>cheers,
>Christoph
>
>On 07/05/2012 06:18 PM, Carson Holt wrote:
>> Your cluster is apparently using the CPAN module local::lib to define
>> where perl libraries and executables get installed, this is overriding
>> MAKER's own installation parameters, thus putting things in the wrong
>> place.  This only happens in 2.10, the 2.25 version of MAKER knows how
>>to
>> keep local::lib from messing with it's relative installation paths.  So
>> install 2.25 and make sure to remove the mis-located MAKER executables
>>in
>> /xanadu/site/common/VERSIONS/perl-1.7/bin/ before trying to run again.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 12-07-05 11:06 AM, "Christoph Hahn" <chrisi.hahni at gmail.com> wrote:
>>
>>> Dear MAKER developers and users,
>>>
>>> I am new to MAKER and during my first attempts I unfortunately
>>> encountert some problems. It would be great if anyone could help me
>>>out!
>>> Here's my problem:
>>> I have used gm_es.pl from Genemark to create es.mod for my assembly. I
>>> would like to give this model to MAKER, so I add the path to es.mod in
>>> the maker_opts.ctl file at gmhmm. So far so good. Unfortunately, when I
>>> am running maker it cannot find the gmhmm_wrap script. Here s what it
>>> says:
>>>
>>> #-------------------------------#
>>> Can't open perl script
>>> 
>>>"/xanadu/site/common/VERSIONS/perl-1.7/bin/../lib/Widget/genemark/gmhmm_
>>>wr
>>> ap":
>>> No such file or directory
>>> ERROR: Genemark failed
>>>
>>> Apparently it is looking for the script in the wrong place. I have
>>>found
>>> it in:
>>> /site/VERSIONS/perl-1.7/perl/lib/MAKER/Widget/genemark/gmhmm_wrap
>>> The other paths are correct.
>>>
>>> Is there a way to manually tell Maker where to look for this script? I
>>> should mention also that I have maker (2.10) running on a cluster.
>>>
>>> Any help is highly appreciated! Thanks in advance!!
>>>
>>> much obliged,
>>> Christoph
>>>
>>> University of Oslo
>>>
>>> _______________________________________________
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>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>
>