[maker-devel] change the PATH to gmhmm_wrap

[Christoph Hahn]

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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>