change program locations in maker_exe

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change program locations in maker_exe

USFS Ion PGM
Hello,
I was wondering if there is a way to make permanent changes to the maker_exe.ctl file, as it seems on the install that maker didn’t find the gene mark or pro build locations correctly, which means that I have to manually edit the maker_exe.ctl file every time and add that information.  Where can I modify this permanently so that the maker -CTL command creates the appropriate maker_exe file?  Thank you.

- Jon


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Re: change program locations in maker_exe

Carson Hinton Holt
MAKER first looks inside of .../maker/exe/ for any executables.  Then it
uses the systems ‘which’ command to identify executables in your PATH
environmental variable.  If MAKER is not finding the one you want, then
you can either put the program in the .../maker/exe/ folder (I.e. create
.../maker/exe/bin/  and then put soft links to the executables you want to
be used first), or you can rearrange the order of paraameters in your PATH
environmental variable so that ‘which <program_name>’ returns the location
you want.  If MAKER is always leaving the locations to those programs
empty, it is because you need to add them to your PATH environmental
variable.

Thanks,
Carson

On 2/26/14, 9:21 AM, "USFS Ion PGM" <[hidden email]> wrote:

>Hello,
>I was wondering if there is a way to make permanent changes to the
>maker_exe.ctl file, as it seems on the install that maker didn’t find the
>gene mark or pro build locations correctly, which means that I have to
>manually edit the maker_exe.ctl file every time and add that information.
> Where can I modify this permanently so that the maker -CTL command
>creates the appropriate maker_exe file?  Thank you.
>
>- Jon
>
>

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Re: change program locations in maker_exe

USFS Ion PGM
Hi Carson,

Thank you - that did it, I didn’t have them in the PATH.  All working now.

Cheers,
Jon

On Feb 26, 2014, at 10:38 AM, Carson Holt <[hidden email]> wrote:

> MAKER first looks inside of .../maker/exe/ for any executables.  Then it
> uses the systems ‘which’ command to identify executables in your PATH
> environmental variable.  If MAKER is not finding the one you want, then
> you can either put the program in the .../maker/exe/ folder (I.e. create
> .../maker/exe/bin/  and then put soft links to the executables you want to
> be used first), or you can rearrange the order of paraameters in your PATH
> environmental variable so that ‘which <program_name>’ returns the location
> you want.  If MAKER is always leaving the locations to those programs
> empty, it is because you need to add them to your PATH environmental
> variable.
>
> Thanks,
> Carson
>
> On 2/26/14, 9:21 AM, "USFS Ion PGM" <[hidden email]> wrote:
>
>> Hello,
>> I was wondering if there is a way to make permanent changes to the
>> maker_exe.ctl file, as it seems on the install that maker didn’t find the
>> gene mark or pro build locations correctly, which means that I have to
>> manually edit the maker_exe.ctl file every time and add that information.
>> Where can I modify this permanently so that the maker -CTL command
>> creates the appropriate maker_exe file?  Thank you.
>>
>> - Jon
>>
>>
>


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