[maker-devel] change the PATH to gmhmm_wrap

[Christoph Hahn]

Dear Carson,

I have installed MAKER 2.25 locally on the cluster now and as you have 
predicted the problem disappeared.
Thanks again for your help!!

cheers,
Christoph


On 07/05/2012 07:00 PM, Carson Holt wrote:
> 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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>>
>