gmod-ajax

[Gmod-ajax] Tutorial out of date?

[Martin A. H. <ma...@ma...>]

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

Re: [Gmod-ajax] Tutorial out of date?

[Martin A. H. <ma...@ma...>]

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outdated.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
>

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
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus
> on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>



-- 
Please keep responses on the list!
http://gmod.org/wiki/January_2010_GMOD_Meeting
http://gmod.org/wiki/GMOD_News
Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback

Re: [Gmod-ajax] Tutorial out of date?

[Mitch S. <mit...@be...>]

Martin A. Hansen wrote:
> The problem is you need to use the source fetched with git. The 
> tarball is outdated.

Again, where did you get the tarball from?

The right way to get a tarball is from github; go to
http://github.com/jbrowse/jbrowse

and click on the "download" button.  I just tried it out, and it was the 
current version.

Mitch

Re: [Gmod-ajax] Tutorial out of date?

[Martin A. H. <ma...@ma...>]

Yup, that is exactly where I downloaded from - and the tarball was funny.
Now I use a clone from GIT and there is no trouble.

How do you determine current version? Is there a version/revision number?


Martin

On Fri, Nov 20, 2009 at 7:09 AM, Mitch Skinner
<mit...@be...>wrote:

> Martin A. Hansen wrote:
>
>> The problem is you need to use the source fetched with git. The tarball is
>> outdated.
>>
>
> Again, where did you get the tarball from?
>
> The right way to get a tarball is from github; go to
> http://github.com/jbrowse/jbrowse
>
> and click on the "download" button.  I just tried it out, and it was the
> current version.
>
> Mitch
>

Re: [Gmod-ajax] Tutorial out of date?

[Mitch S. <mit...@be...>]

On 11/19/2009 11:13 PM, Martin A. Hansen wrote:
> Yup, that is exactly where I downloaded from - and the tarball was 
> funny. Now I use a clone from GIT and there is no trouble.

Hmmm, I haven't been able to reproduce this, so I'm not sure where to go 
from here.  If anyone else encounters this please let me know.

> How do you determine current version? Is there a version/revision number?

We haven't started tagging versions yet, but tarball downloads and git 
clones do come with mechanisms that allow you to identify the current 
commit.

If you get a tarball, the tarball name has the first part of the commit 
hash in it.  In the example below, "020db6d" identifies the version.

If you have a git clone, you can do a "git rev-parse HEAD" to get the 
hash of the current head commit.

Mitch

$ wget http://github.com/jbrowse/jbrowse/tarball/master
--2009-11-20 09:10:15--  http://github.com/jbrowse/jbrowse/tarball/master
Resolving github.com... 207.97.227.239
Connecting to github.com|207.97.227.239|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: http://waitdownload.github.com/jbrowse-jbrowse-020db6d.tar.gz 
[following]
--2009-11-20 09:10:16--  
http://waitdownload.github.com/jbrowse-jbrowse-020db6d.tar.gz
Resolving waitdownload.github.com... 207.97.227.241
Connecting to waitdownload.github.com|207.97.227.241|:80... connected.
HTTP request sent, awaiting response... 302 Moved Temporarily
Location: http://download.github.com/jbrowse-jbrowse-020db6d.tar.gz 
[following]
--2009-11-20 09:10:17--  
http://download.github.com/jbrowse-jbrowse-020db6d.tar.gz
Resolving download.github.com... 207.97.227.240
Connecting to download.github.com|207.97.227.240|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 509686 (498K) [application/octet-stream]
Saving to: `jbrowse-jbrowse-020db6d.tar.gz'

100%[======================================>] 509,686      236K/s   in 2.1s

2009-11-20 09:10:21 (236 KB/s) - `jbrowse-jbrowse-020db6d.tar.gz' saved 
[509686/509686]

$ ls
jbrowse-jbrowse-020db6d.tar.gz