[maker-devel] How to make maker output into another directory

[Carson Holt]

Just make the desired path be your working directory then use -base to specify a name for the maker.output directory.

—Carson

Sent from my iPhone

> On Oct 1, 2019, at 11:15 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> 
> Hi Carson
> Thanks for your email
> 
> I tried to use the -base option to make maker output into a new directory /mnt/data/emmanuel/Makersupport/mucuna
> 
> The log report is found below 
> 
> The 'base' option is an ID used in generating names for
> multiple files and directories. It is not a directory path.
> You must remove all '/' characters from '/mnt/data/emmanuel/Makersupport/mucuna'
> 
> Thanks
> 
> Emmanuel
> 
> Nnadi Nnaemeka Emmanuel,Ph.D
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> +2348068124819
> Publications: 
>  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
> 
> 
>> On Tue, Oct 1, 2019 at 5:34 PM Carson Holt <carsonhh at gmail.com> wrote:
>> 
>> 
>>> On Oct 1, 2019, at 7:59 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
>>> 
>>> Hi Carson
>>> I want marker to output into a directory  /mnt/data/emmanuel/Makersupport. Please how can I make that?
>> 
>> 
>> 
>> From the usage statement —>
>> 
>>      -base    <string>   Set the base name MAKER uses to save output files.
>>                                   MAKER uses the input genome file name by default.
>> 
>> 
>> 
>>> 
>>> 
>>> Also,
>>> 
>>> I added RepBaseRepeatMaskerEdition-20170127.tar into the directory /home/emmanuel/maker/exe/RepeatMasker
>>> 
>>> used tar xvf RepBaseRepeatMaskerEdition-20170127.tar to unpack it. In my /home/emmanuel/maker/exe/RepeatMasker/Libraries I have RMRBSeqs.embl  but running maker it tells me it repbase is not installed.
>> 
>> 
>> After uncaring RepBase you have to run the ./configure script with rmblast installed and it will create the needed blast indexes and libraries
>> 
>> RepeatMasker.lib
>> RepeatMaskerLib.embl
>> RepeatMasker.lib.nhr
>> RepeatMasker.lib.nin
>> RepeatMasker.lib.nsq
>> RepeatMasker.lib.xnd
>> RepeatMasker.lib.xni
>> RepeatMasker.lib.xns
>> RepeatMasker.lib.xnt
>> RepeatPeps.lib
>> RepeatPeps.lib.phr
>> RepeatPeps.lib.pin
>> RepeatPeps.lib.psq
>> RepeatPeps.lib.xpd
>> RepeatPeps.lib.xpi
>> RepeatPeps.lib.xps
>> RepeatPeps.lib.xpt
>> 
>> 
>> —Carson
>> 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20191002/743a6e79/attachment-0004.html>