Re: [Gmod-ajax] Tutorial out of date?

[Dave C. G. H. D. <he...@gm...>]

Hi Martin,

If grabbing the source with GIT doesn't do the trick for you, there is
also a tutorial at
http://gmod.ork/wiki/JBrowse_Tutorial, which was written this August.

Dave C.

On Sat, Nov 14, 2009 at 4:27 PM, Martin A. Hansen <ma...@ma...> wrote:
> The problem is you need to use the source fetched with git. The tarball is
> outdated.
>
>
> Martin
>
> On Sat, Nov 14, 2009 at 3:10 PM, Martin A. Hansen <ma...@ma...> wrote:
>>
>> I grabbed a fresh copy of Jbrowse and set about to install the test data
>> following the tutorial:
>>
>> http://jbrowse.org/code/jbrowse-master/docs/tutorial/
>>
>> However, at step one:
>>
>> bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa
>>
>> Unknown option: fasta
>> USAGE:
>>        bin/prepare-refseqs.pl [--out <output directory>] --gff <gff file
>> describing refseqs>
>>    OR:
>>        bin/prepare-refseqs.pl [--out <output directory>] [--noseq]
>> [--seqdir <sequence data directory>] --conf <JBrowse config file> --refs
>> <list of refseq names> --refids <list of refseq IDs>
>>     <output directory>: defaults to "data"
>>     <sequence data directory>: chunks of sequence go here; defaults to
>> "<output directory>/seq"
>>
>>     --noseq: do not prepare sequence data for the client.
>>
>>     You can use a GFF file to describe the reference sequences, or
>>     you can use a JBrowse config file and a list of refseq names
>>     or a list of refseq IDs.  If you use a GFF file, it should
>>     contain ##sequence-region lines as described in the GFF specs.
>>     If you use a JBrowse config file, you can either provide a
>>     (comma-separated) list of refseq names, or (if the names
>>     aren't globally unique) a list of refseq IDs.
>>
>>
>> What is going on?
>>
>>
>>
>> Martin
>
>
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