Fwd: Re: blastGraphic project status

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Fwd: Re: blastGraphic project status

Robert Buels
Also forwarding this thread to gmod-devel so people know.
Bio::GMOD::Blast::Graph* modules have been split out of the BLAST
Graphic Viewer (http://gmod.org/wiki/BLAST_Graphic_Viewer) and pushed to
CPAN.

Rob


-------- Original Message --------
Subject: Re: blastGraphic project status
Date: Thu, 14 Apr 2011 10:52:06 -0700
From: Robert Buels <[hidden email]>
Organization: Sol Genomics Network
To: Benjamin Hitz <[hidden email]>
CC: Jonathan Leto <[hidden email]>, Scott Cain <[hidden email]>,
  Shuai Weng <[hidden email]>

OK, here's what I did:

  1. extracted the Bio::GMOD::Blast::Graph* modules into another dist,
     see https://github.com/gmod/Bio-GMOD-Blast-Graph
  2. wrote some tests for them
  3. fixed some small bugs
  4. made them capable of printing to something other than STDOUT,
     maintaining backcompat default behavior
  5. shipped them to CPAN
        http://search.cpan.org/~rbuels/Bio-GMOD-Blast-Graph-0.02/

The CGI script, conf, and things are still in GMOD svn, and I updated
their Makefile.PL there to give them a dependency on the CPAN modules.
We don't intend to do any further work on the CGI part.

So, in summary, it's split into two parts, the CGI in the GMOD svn,
which we don't plan to touch further, and the modules on GitHub, which
Duke and I can maintain.  Things are on a pretty good footing now I think.

Rob



On 04/13/2011 12:08 PM, Benjamin Hitz wrote:

> Rob -
> We use it - or at least some version of it, but try to avoid touching it.  Not sure our version is the same as what's in SVN.
> Feel free to coopt and clear up as you see fit.
>
> Shuai, the original author has been cc'd if you have any questions.
>
> Ben
>
> On Apr 13, 2011, at 11:08 AM, Robert Buels wrote:
>
>> Hi Ben,
>>
>> http://gmod.svn.sourceforge.net/viewvc/gmod/blastGraphic/trunk/  hasn't been touched in many years.  Are you guys still using it?
>>
>> We'd like to use some of it in Mimosa (https://github.com/gmod/mimosa) but the code really needs a lot of cleaning up, and needs to go on CPAN.
>>
>> Can Duke and I take it over, clean it up, move it to github under GMOD, and push it to CPAN?  We'll keep the authors list of course, and we'll try to keep backcompat.  Although that could be difficult since there are no tests.
>>
>> Rob
>
> --
> Ben Hitz
> Senior Scientific Programmer
> Saccharomyces Genome Project
> Stanford University
> [hidden email]
>
>
>
>


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Re: Fwd: Re: blastGraphic project status

Jonathan "Duke" Leto
Howdy,

Thanks for this awesome work, Rob!

This will allow Bio::GMOD::Blast::Graph to be used in Mimosa [0] to
generate graphics in BLAST reports.

Duke

[0] https://github.com/GMOD/mimosa

On Thu, Apr 14, 2011 at 10:55 AM, Robert Buels <[hidden email]> wrote:

> Also forwarding this thread to gmod-devel so people know.
> Bio::GMOD::Blast::Graph* modules have been split out of the BLAST
> Graphic Viewer (http://gmod.org/wiki/BLAST_Graphic_Viewer) and pushed to
> CPAN.
>
> Rob
>
>
> -------- Original Message --------
> Subject: Re: blastGraphic project status
> Date: Thu, 14 Apr 2011 10:52:06 -0700
> From: Robert Buels <[hidden email]>
> Organization: Sol Genomics Network
> To: Benjamin Hitz <[hidden email]>
> CC: Jonathan Leto <[hidden email]>, Scott Cain <[hidden email]>,
>  Shuai Weng <[hidden email]>
>
> OK, here's what I did:
>
>  1. extracted the Bio::GMOD::Blast::Graph* modules into another dist,
>     see https://github.com/gmod/Bio-GMOD-Blast-Graph
>  2. wrote some tests for them
>  3. fixed some small bugs
>  4. made them capable of printing to something other than STDOUT,
>     maintaining backcompat default behavior
>  5. shipped them to CPAN
>        http://search.cpan.org/~rbuels/Bio-GMOD-Blast-Graph-0.02/
>
> The CGI script, conf, and things are still in GMOD svn, and I updated
> their Makefile.PL there to give them a dependency on the CPAN modules.
> We don't intend to do any further work on the CGI part.
>
> So, in summary, it's split into two parts, the CGI in the GMOD svn,
> which we don't plan to touch further, and the modules on GitHub, which
> Duke and I can maintain.  Things are on a pretty good footing now I think.
>
> Rob
>
>
>
> On 04/13/2011 12:08 PM, Benjamin Hitz wrote:
>> Rob -
>> We use it - or at least some version of it, but try to avoid touching it.  Not sure our version is the same as what's in SVN.
>> Feel free to coopt and clear up as you see fit.
>>
>> Shuai, the original author has been cc'd if you have any questions.
>>
>> Ben
>>
>> On Apr 13, 2011, at 11:08 AM, Robert Buels wrote:
>>
>>> Hi Ben,
>>>
>>> http://gmod.svn.sourceforge.net/viewvc/gmod/blastGraphic/trunk/  hasn't been touched in many years.  Are you guys still using it?
>>>
>>> We'd like to use some of it in Mimosa (https://github.com/gmod/mimosa) but the code really needs a lot of cleaning up, and needs to go on CPAN.
>>>
>>> Can Duke and I take it over, clean it up, move it to github under GMOD, and push it to CPAN?  We'll keep the authors list of course, and we'll try to keep backcompat.  Although that could be difficult since there are no tests.
>>>
>>> Rob
>>
>> --
>> Ben Hitz
>> Senior Scientific Programmer
>> Saccharomyces Genome Project
>> Stanford University
>> [hidden email]
>>
>>
>>
>>
>
>
> ------------------------------------------------------------------------------
> Benefiting from Server Virtualization: Beyond Initial Workload
> Consolidation -- Increasing the use of server virtualization is a top
> priority.Virtualization can reduce costs, simplify management, and improve
> application availability and disaster protection. Learn more about boosting
> the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev
> _______________________________________________
> Gmod-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>



--
Jonathan "Duke" Leto
[hidden email]
http://leto.net

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Mimosa

Benjamin Hitz-2

Hey, does Mimosa handle situations where a job is started on a server, but may take a (very) log time to return?
E.g.: http://www.ebi.ac.uk/Tools/sss/wublast/

Which uses DWR (Javascript/Java interface for job scheduling).  But Java, bleah.     I don't need a queueing system, I just need to submit jobs (remotely?), create a link back to the results (when done!) and poll (via AJAX) if they leave the window open.  

We have stuff like this around, but it's super hacky old school CGI stuff.  

Ben
--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
Stanford University ** [hidden email]





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Re: Mimosa

Jonathan "Duke" Leto
Howdy,

You can see the current list of stuff we are working on in Mimosa here:

https://github.com/GMOD/mimosa/issues

Since SGN uses qsub and I am in the process of migrating the SGN websites blast
tool to use Mimosa, integration with submitting jobs via qsub will probably be
worked on first. There is a stub of a ticket for it here:

https://github.com/GMOD/mimosa/issues/68

Sadly, I have some other issues that I am working on in the near term:

https://github.com/GMOD/mimosa/issues?sort=updated&labels=important&direction=desc&state=open

That being said, it would be superbly awesome if you had some tuits to
add qsub or some other job queue support. The place to start is right
here:

https://github.com/GMOD/mimosa/blob/master/lib/App/Mimosa/Job.pm#L138

Basically, the way Mimosa works is that it has a job table in a database. When
the job is marked as done, the web interface presents the web user with the
alignment report they are looking for, which is identified by a sha1 or report
number. If it isn't marked as done, it tells the web user the job is still
running.

If you are interested in playing around with Mimosa and you want to set up an
instance to play around with, please let me know.

Duke

On Mon, Sep 26, 2011 at 4:02 PM, Benjamin Hitz <[hidden email]> wrote:

>
> Hey, does Mimosa handle situations where a job is started on a server, but may take a (very) log time to return?
> E.g.: http://www.ebi.ac.uk/Tools/sss/wublast/
>
> Which uses DWR (Javascript/Java interface for job scheduling).  But Java, bleah.     I don't need a queueing system, I just need to submit jobs (remotely?), create a link back to the results (when done!) and poll (via AJAX) if they leave the window open.
>
> We have stuff like this around, but it's super hacky old school CGI stuff.
>
> Ben
> --
> Ben Hitz
> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
> Stanford University ** [hidden email]
>
>
>
>
>

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