[maker-devel] Problem with installation

[Panos Ioannidis]

So I managed to install it on my workstation and it works fine! Thanks for
the information on perlbrew. I will also give it a try.

I did a test run on my workstation using just a few contigs and was
wondering where the annotation is saved. Is it the gff files (one gff per
contig) in the *.maker.output/ directory?




On Wed, May 28, 2014 at 6:28 PM, Carson Holt <carsonhh at gmail.com> wrote:

> Try perlbrew to set up yor own local version of perl just for your user.
> http://perlbrew.pl
>
> --Carson
>
>
> From: Panos Ioannidis <panos.ioannidis at gmail.com>
> Date: Wednesday, May 28, 2014 at 10:13 AM
> To: Carson Holt <carsonhh at gmail.com>
> Cc: Daniel Ence <dence at genetics.utah.edu>, "<maker-devel at yandell-lab.org>"
> <maker-devel at yandell-lab.org>
>
> Subject: Re: [maker-devel] Problem with installation
>
> Hello Daniel and Carson,
>
> Thank you both for your comments.
>
> Carson, I gave it a lot more than 30 seconds. I gave it about 5 minutes
> but still nothing happens.
>
> Daniel, the same is true for maker -CTL; it appears as if it's doing
> something, but if you give a top you'll see that the CPU usage is ALWAYS
> 0%.
>
> Three things that might be helpful:
> 1. Ctrl-C doesn't work for killing maker; you have to give "kill -9 <PID>"
> 2. when I give top I see that there are two maker processes running. Is
> this normal?
> 3. When I press Ctrl-C, the resources in top (labeled VIRT, RES and SHR -
> I guess that's memory) for one of the two maker processes go to zero, but
> it doesn't go away.
>
>
>
>
>
> On Wed, May 28, 2014 at 4:32 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> Perl is a scripting language rather than a compiled language, and one
>> thing that happens when you first use a new module or script Is that the
>> interpreter follows the dependency tree validating that everything
>> executes/loads correctly.  Since you installed a number of dependencies and
>> MAKER itself, the first time you launch MAKER Perl has to do this check on
>> the dependency tree.  This only happens the first time, and after that Perl
>> remembers it already ran the check so the dependencies and MAKER will just
>> start from then on.  Normally this proccess takes less than 30 seconds;
>> however, on some systems (especially clusters) there may a  heavy IO burden
>> and this process can take a while.  For example does it take a moment for
>> 'ls -al' to return in some directories rather than returning
>> instantaneously like it is supposed to?  If it takes 3 seconds to return or
>> example, then each dependency check may take up to 3 seconds.  If you just
>> installed a bunch of new perl modules then there may be a hundred or more
>> dependencies that may have to be validated for the first time.
>>
>> --Carson
>>
>>
>>
>> From: Daniel Ence <dence at genetics.utah.edu>
>> Date: Wednesday, May 28, 2014 at 7:29 AM
>> To: Panos Ioannidis <panos.ioannidis at gmail.com>
>> Cc: "<maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org>
>> Subject: Re: [maker-devel] Problem with installation
>>
>> Hi Panos, When you go to the src directory and type "./Build status",
>> what message do you get? Also, what version of maker are you running?
>>
>> Thanks,
>> Daniel
>>
>>
>> Daniel Ence
>> Graduate Student
>> dence at genetics.utah.edu
>> Eccles Institute of Human Genetics
>> University of Utah
>> 15 North 2030 East, Room 2100
>> Salt Lake City, UT 84112-5330
>>
>> On May 28, 2014, at 1:28 AM, Panos Ioannidis <panos.ioannidis at gmail.com>
>>  wrote:
>>
>> Hello Maker community,
>>
>> I just finished installing Maker and even though everything seems to be
>> okay, when I give
>>
>> ./maker -h
>>
>> or
>>
>> ./maker
>>
>> the program apparently hangs without giving any output or warning or
>> error.
>>
>> Just so you know, I have installed all dependencies (Perl libraries and
>> third-party programs) and am executing from bin/, not src/bin/.
>>
>> Any ideas?
>>
>> Panos
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>>
>>
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>>
>
>
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