How to make maker output into another directory

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How to make maker output into another directory

Emmanuel Nnadi
Hi Carson
I want marker to output into a directory  /mnt/data/emmanuel/Makersupport. Please how can I make that?

OPTS=/home/emmanuel/maker/bin

BOPTS=/home/emmanuel/maker/bin

EXE=/home/emmanuel/maker/bin

MAKER=/home/emmanuel/maker/bin

OUT=/mnt/data/emmanuel/Makersupport


${MAKER}/maker  -cpus 26 ${OPTS}/maker_opts.ctl ${BOPTS}/maker_bopts.ctl ${EXE}/maker_exe.ctl



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.

Nnadi Nnaemeka Emmanuel,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications: 

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Re: How to make maker output into another directory

Carson Holt-2


On Oct 1, 2019, at 7:59 AM, Emmanuel Nnadi <[hidden email]> 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


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Re: How to make maker output into another directory

Emmanuel Nnadi
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: 


On Tue, Oct 1, 2019 at 5:34 PM Carson Holt <[hidden email]> wrote:


On Oct 1, 2019, at 7:59 AM, Emmanuel Nnadi <[hidden email]> 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


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Re: How to make maker output into another directory

Carson Holt-2
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 <[hidden email]> 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: 


On Tue, Oct 1, 2019 at 5:34 PM Carson Holt <[hidden email]> wrote:


On Oct 1, 2019, at 7:59 AM, Emmanuel Nnadi <[hidden email]> 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


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maker-devel mailing list
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http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org