Re: [Gmod-ajax] maker2jbrowse Can't exec "prepare-refseqs.pl":

[Scott C. <sc...@sc...>]

Hi Flora,

I haven't used maker2jbrowse, but my naive suggestion is to try executing
maker2jbrowse from one directory up (so in the main jbrowse directory),
like:

  bin/maker2jbrowse <gff path>

The only reason I suggest this is that's how I execute every other script
that I use in JBrowse. There might be a built in assumption about where
it's getting executed from.

Scott


On Fri, Aug 19, 2022 at 9:58 AM Flora Uesseler <
flo...@un...> wrote:

> Dear GMOD Team,
>
> I am trying to parse my maker-derived GFF to jbrowse with maker2jbrowse,
> but keep running into the below issue.
>
> ./maker2jbrowse ~/annotation-workdir/maker-rounds/rnd2_v2.summary.gff
>> Can't exec "prepare-refseqs.pl": No such file or directory at
>> ./maker2jbrowse line 280.
>> prepare-refseqs.pl failed with exit status -1 at ./maker2jbrowse line
>> 280.
>>
>
> I managed to run prepare-refseqs.pl on its own succesfully.
> Can you advise a way around this error?
>
> The version I am using is JBrowse-1.16.11, downloaded as a zipfile from
> https://jbrowse.org/blog/
> I just unzipped and tried using the maker2jbrowse script in the /bin
> directory. I tried both with the minified release and the dev version.
>
> My best,
> Flora
>
>
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott
at scottcain dot net
GMOD Project Manager (http://gmod.org/)
216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (
https://hcmi-searchable-catalog.nci.nih.gov/)