[maker-devel] change the PATH to gmhmm_wrap

[Carson Holt]

I'm glad it's working.

Thanks,
Carson



On 12-07-06 12:03 PM, "Christoph Hahn" <chrisi.hahni at gmail.com> wrote:

>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/gmhm
>>>>>m_
>>>>> 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
>>>>>
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>>
>>
>
>