[Gmod-ajax] jbrowse-plugins repo?

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[Gmod-ajax] jbrowse-plugins repo?

Scott Cain
Hi Eric,

Do you have any interest in having a jbrowse-plugins repo in GMOD's github account?  It seems like having a place to put them is a good idea, but I'm good with the decentralized way it is now too.

I can't think of any downsides, but there probably are and they just haven't occurred to me.

Scott


--
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
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reports.http://sdm.link/zohodev2dev
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Re: jbrowse-plugins repo?

Eric Yao
Hi Scott,
I'm trying to work this out now.  There's a possible contender for a jBrowse registry code, which I hope can work out.
However, I'm open to such suggestions.
Arguments?
Thanks,
Eric


On Fri, Jul 15, 2016 at 11:06 AM, Scott Cain <[hidden email]> wrote:
Hi Eric,

Do you have any interest in having a jbrowse-plugins repo in GMOD's github account?  It seems like having a place to put them is a good idea, but I'm good with the decentralized way it is now too.

I can't think of any downsides, but there probably are and they just haven't occurred to me.

Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
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Re: jbrowse-plugins repo?

Eric Rasche-3
Not scott, but my 2cents:
  • centralized place requiring zero infrastructure and maintenance.
  • could be opened up to community moderation/maintenance, allow them to maintain plugins that would otherwise be abandoned
    • (this model works in galaxy with the IUC maintaining old tools and updating their interfaces when necessary)

On 15. juli 2016 18:22, Eric Yao wrote:
Hi Scott,
I'm trying to work this out now.  There's a possible contender for a jBrowse registry code, which I hope can work out.
However, I'm open to such suggestions.
Arguments?
Thanks,
Eric


On Fri, Jul 15, 2016 at 11:06 AM, Scott Cain <[hidden email]> wrote:
Hi Eric,

Do you have any interest in having a jbrowse-plugins repo in GMOD's github account?  It seems like having a place to put them is a good idea, but I'm good with the decentralized way it is now too.

I can't think of any downsides, but there probably are and they just haven't occurred to me.

Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev


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Center for Phage Technology
Rm 312A, Biochemistry & Biophysics
Texas A&M University
College Station, TX 77843
[hidden email]

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
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Re: jbrowse-plugins repo?

Eric Rasche-3
In reply to this post by Eric Yao
Not scott, but my 2cents:
  • centralized place requiring zero infrastructure and maintenance.
  • could be opened up to community moderation/maintenance, allow them to maintain plugins that would otherwise be abandoned
    • (this model works in galaxy with the IUC maintaining old tools and updating their interfaces when necessary)

On 15. juli 2016 18:22, Eric Yao wrote:
Hi Scott,
I'm trying to work this out now.  There's a possible contender for a jBrowse registry code, which I hope can work out.
However, I'm open to such suggestions.
Arguments?
Thanks,
Eric


On Fri, Jul 15, 2016 at 11:06 AM, Scott Cain <[hidden email]> wrote:
Hi Eric,

Do you have any interest in having a jbrowse-plugins repo in GMOD's github account?  It seems like having a place to put them is a good idea, but I'm good with the decentralized way it is now too.

I can't think of any downsides, but there probably are and they just haven't occurred to me.

Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev


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Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, Biochemistry & Biophysics
Texas A&M University
College Station, TX 77843
[hidden email]

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
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Re: jbrowse-plugins repo?

Eric Yao
Thanks,
How is what gets into the public toolshed managed?

On Fri, Jul 15, 2016 at 11:29 AM, Eric Rasche <[hidden email]> wrote:
Not scott, but my 2cents:
  • centralized place requiring zero infrastructure and maintenance.
  • could be opened up to community moderation/maintenance, allow them to maintain plugins that would otherwise be abandoned
    • (this model works in galaxy with the IUC maintaining old tools and updating their interfaces when necessary)

On 15. juli 2016 18:22, Eric Yao wrote:
Hi Scott,
I'm trying to work this out now.  There's a possible contender for a jBrowse registry code, which I hope can work out.
However, I'm open to such suggestions.
Arguments?
Thanks,
Eric


On Fri, Jul 15, 2016 at 11:06 AM, Scott Cain <[hidden email]> wrote:
Hi Eric,

Do you have any interest in having a jbrowse-plugins repo in GMOD's github account?  It seems like having a place to put them is a good idea, but I'm good with the decentralized way it is now too.

I can't think of any downsides, but there probably are and they just haven't occurred to me.

Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev


_______________________________________________
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--
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, Biochemistry & Biophysics
Texas A&M University
College Station, TX 77843
[hidden email]


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
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Re: jbrowse-plugins repo?

Eric Rasche-3
Travis.
https://github.com/galaxyproject/tools-iuc/blob/master/.travis.yml#L52

On 15. juli 2016 18:35, Eric Yao wrote:
Thanks,
How is what gets into the public toolshed managed?

On Fri, Jul 15, 2016 at 11:29 AM, Eric Rasche <[hidden email]> wrote:
Not scott, but my 2cents:
  • centralized place requiring zero infrastructure and maintenance.
  • could be opened up to community moderation/maintenance, allow them to maintain plugins that would otherwise be abandoned
    • (this model works in galaxy with the IUC maintaining old tools and updating their interfaces when necessary)

On 15. juli 2016 18:22, Eric Yao wrote:
Hi Scott,
I'm trying to work this out now.  There's a possible contender for a jBrowse registry code, which I hope can work out.
However, I'm open to such suggestions.
Arguments?
Thanks,
Eric


On Fri, Jul 15, 2016 at 11:06 AM, Scott Cain <[hidden email]> wrote:
Hi Eric,

Do you have any interest in having a jbrowse-plugins repo in GMOD's github account?  It seems like having a place to put them is a good idea, but I'm good with the decentralized way it is now too.

I can't think of any downsides, but there probably are and they just haven't occurred to me.

Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev


_______________________________________________
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--
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, Biochemistry & Biophysics
Texas A&M University
College Station, TX 77843
[hidden email]


--

Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
<a href="tel:404-692-2048">404-692-2048
[hidden email]
Not responding quickly enough?

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
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Re: jbrowse-plugins repo?

nathandunn
In reply to this post by Scott Cain

I just wanted to clarify if you were wanting to create a single repos for all of the plugins?  

I think we need the model of having a single repo per plugin (but talk me out of it).   Having something centralized that points back to the originating (likely decentralized) repos is good (similar to the galaxy toolshed link that Eric sent out), as well as having individual plugins exist under the GMOD account that are “more official” (similar to an approved Galaxy IUC plugin) might be good, but not necessary.    

Nathan

On Jul 15, 2016, at 11:06 AM, Scott Cain <[hidden email]> wrote:

Hi Eric,

Do you have any interest in having a jbrowse-plugins repo in GMOD's github account?  It seems like having a place to put them is a good idea, but I'm good with the decentralized way it is now too.

I can't think of any downsides, but there probably are and they just haven't occurred to me.

Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
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Re: jbrowse-plugins repo?

Scott Cain
I mostly want people to be able to find plugins.  Andrew Wilkey created a directory:


which seems like a step in the right direction.  A toolshed seems nice too, as long as somebody sets it up.  

In addition, it would be nice for developers to have a place to put them if they didn't know where else to put them.  I'm not convinced that it should necessarily be one plugin--one repo, but I can see the instinct that points that way.  The GBrowse data adaptors repo (GBrowse-adaptors) has multiple adaptors in it (3 or 4) but then, those are only maintained by Lincoln and me.

On Fri, Jul 15, 2016 at 3:41 PM, Nathan Dunn <[hidden email]> wrote:

I just wanted to clarify if you were wanting to create a single repos for all of the plugins?  

I think we need the model of having a single repo per plugin (but talk me out of it).   Having something centralized that points back to the originating (likely decentralized) repos is good (similar to the galaxy toolshed link that Eric sent out), as well as having individual plugins exist under the GMOD account that are “more official” (similar to an approved Galaxy IUC plugin) might be good, but not necessary.    

Nathan

On Jul 15, 2016, at 11:06 AM, Scott Cain <[hidden email]> wrote:

Hi Eric,

Do you have any interest in having a jbrowse-plugins repo in GMOD's github account?  It seems like having a place to put them is a good idea, but I'm good with the decentralized way it is now too.

I can't think of any downsides, but there probably are and they just haven't occurred to me.

Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
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Re: jbrowse-plugins repo?

nathandunn

On Jul 15, 2016, at 12:56 PM, Scott Cain <[hidden email]> wrote:

I mostly want people to be able to find plugins.  Andrew Wilkey created a directory:


which seems like a step in the right direction.  A toolshed seems nice too, as long as somebody sets it up.  

This is very nice (thank you Andrew!).   I think the only difference would be putting the site source on github and managing the site as another github/GMOD project, but I think the overall theme is great.    Allowing users to register, login, edit, their entries, etc. would be ideal.  

In addition, it would be nice for developers to have a place to put them if they didn't know where else to put them.  I'm not convinced that it should necessarily be one plugin--one repo, but I can see the instinct that points that way.  The GBrowse data adaptors repo (GBrowse-adaptors) has multiple adaptors in it (3 or 4) but then, those are only maintained by Lincoln and me.

I’d like the option to install the plugins via bower (or a similar package manager) if desired at some point so that a user could easily switch branches, versions, repos, etc. with minimal work.   Its kind of what we’re hacking in now on top of JBrowse and it works okay.  

Nathan


On Fri, Jul 15, 2016 at 3:41 PM, Nathan Dunn <[hidden email]> wrote:

I just wanted to clarify if you were wanting to create a single repos for all of the plugins?  

I think we need the model of having a single repo per plugin (but talk me out of it).   Having something centralized that points back to the originating (likely decentralized) repos is good (similar to the galaxy toolshed link that Eric sent out), as well as having individual plugins exist under the GMOD account that are “more official” (similar to an approved Galaxy IUC plugin) might be good, but not necessary.    

Nathan

On Jul 15, 2016, at 11:06 AM, Scott Cain <[hidden email]> wrote:

Hi Eric,

Do you have any interest in having a jbrowse-plugins repo in GMOD's github account?  It seems like having a place to put them is a good idea, but I'm good with the decentralized way it is now too.

I can't think of any downsides, but there probably are and they just haven't occurred to me.

Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank" class="">216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
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Re: jbrowse-plugins repo?

AWilkey
The source is available here, actually, if not exactly perfect yet (threw the thing together over a weekend before the galaxy community conference as an excuse to play with deploying a full MEAN stack and to play with angular)

https://github.com/awilkey/pluginapp

That being said, there are plans afoot to add user auth and possibly to make a stand-alone local version that  can be put in a jbrowse directory and grab selected plugins via bower.


On Fri, Jul 15, 2016 at 3:29 PM, Nathan Dunn <[hidden email]> wrote:

On Jul 15, 2016, at 12:56 PM, Scott Cain <[hidden email]> wrote:

I mostly want people to be able to find plugins.  Andrew Wilkey created a directory:


which seems like a step in the right direction.  A toolshed seems nice too, as long as somebody sets it up.  

This is very nice (thank you Andrew!).   I think the only difference would be putting the site source on github and managing the site as another github/GMOD project, but I think the overall theme is great.    Allowing users to register, login, edit, their entries, etc. would be ideal.  

In addition, it would be nice for developers to have a place to put them if they didn't know where else to put them.  I'm not convinced that it should necessarily be one plugin--one repo, but I can see the instinct that points that way.  The GBrowse data adaptors repo (GBrowse-adaptors) has multiple adaptors in it (3 or 4) but then, those are only maintained by Lincoln and me.

I’d like the option to install the plugins via bower (or a similar package manager) if desired at some point so that a user could easily switch branches, versions, repos, etc. with minimal work.   Its kind of what we’re hacking in now on top of JBrowse and it works okay.  

Nathan


On Fri, Jul 15, 2016 at 3:41 PM, Nathan Dunn <[hidden email]> wrote:

I just wanted to clarify if you were wanting to create a single repos for all of the plugins?  

I think we need the model of having a single repo per plugin (but talk me out of it).   Having something centralized that points back to the originating (likely decentralized) repos is good (similar to the galaxy toolshed link that Eric sent out), as well as having individual plugins exist under the GMOD account that are “more official” (similar to an approved Galaxy IUC plugin) might be good, but not necessary.    

Nathan

On Jul 15, 2016, at 11:06 AM, Scott Cain <[hidden email]> wrote:

Hi Eric,

Do you have any interest in having a jbrowse-plugins repo in GMOD's github account?  It seems like having a place to put them is a good idea, but I'm good with the decentralized way it is now too.

I can't think of any downsides, but there probably are and they just haven't occurred to me.

Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev_______________________________________________
Gmod-ajax mailing list
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
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E: [hidden email]
O: 0023 CGIL

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What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
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Re: jbrowse-plugins repo?

Eric Rasche-3


On 15. juli 2016 20:35, Andrew Wilkey wrote:
The source is available here, actually, if not exactly perfect yet (threw the thing together over a weekend before the galaxy community conference as an excuse to play with deploying a full MEAN stack and to play with angular)

https://github.com/awilkey/pluginapp

That being said, there are plans afoot to add user auth and possibly to make a stand-alone local version that  can be put in a jbrowse directory and grab selected plugins via bower.


On Fri, Jul 15, 2016 at 3:29 PM, Nathan Dunn <[hidden email]> wrote:

On Jul 15, 2016, at 12:56 PM, Scott Cain <[hidden email]> wrote:

I mostly want people to be able to find plugins.  Andrew Wilkey created a directory:


which seems like a step in the right direction.  A toolshed seems nice too, as long as somebody sets it up.
Toolshed == plugin directory, you shouldn't reuse the galaxy toolshed for anything other than galaxy (it's just not suited to it, it's too Galaxy specific).
 

This is very nice (thank you Andrew!).   I think the only difference would be putting the site source on github and managing the site as another github/GMOD project, but I think the overall theme is great.    Allowing users to register, login, edit, their entries, etc. would be ideal. 
Andrew has done great work on this, but I think if GMOD really want a plugin repository, they should really, strongly consider whether they needs such infrastructure as a MEAN stack. I would provide the counterpoint here of a number of galaxy related repositories which simply have a TSV file listing plugins/datasets/etc. Because your choices are:
  • Run a plugin service
    • Must implement auth, updating plugins, user management logic
    • Travis integration is not trivial if you (e.g.) wanted to make sure plugins were passing some tests
    • Editing entries requires (already implemented) logic for managing things in a database
    • Deployment is manual
    • Must handle service costs (human time deploying, updating, managing OS updates, etc)
  • Stick a TSV file in github
    • Registration/login is done by GH
    • Travis integration is trivial, we can run checks on every plugin regularly.
    • Editing entries is done via pull request and a couple of community moderators
    • Deployment is handled by GH pages, automatically, by clicking a button in the repo config.
    • Free

Galaxy IUC members tend to follow YAGNI pretty seriously, we've replaced a number of what would be traditional database by static sites. We've found that they're far easier to deal with. Need an API? Dump json files in a directory. No URL routing logic needed. No compute power needed.


In addition, it would be nice for developers to have a place to put them if they didn't know where else to put them.  I'm not convinced that it should necessarily be one plugin--one repo, but I can see the instinct that points that way.  The GBrowse data adaptors repo (GBrowse-adaptors) has multiple adaptors in it (3 or 4) but then, those are only maintained by Lincoln and me.
One-plugin per repo has the advantage of being bower installable and that's really, really useful.

Monorepo makes maintenance easier (community volunteers who are updating plugins can update all at once), but at the cost of writing your own plugin manager.

I’d like the option to install the plugins via bower (or a similar package manager) if desired at some point so that a user could easily switch branches, versions, repos, etc. with minimal work.   Its kind of what we’re hacking in now on top of JBrowse and it works okay.  

Nathan


On Fri, Jul 15, 2016 at 3:41 PM, Nathan Dunn <[hidden email]> wrote:

I just wanted to clarify if you were wanting to create a single repos for all of the plugins?  

I think we need the model of having a single repo per plugin (but talk me out of it).   Having something centralized that points back to the originating (likely decentralized) repos is good (similar to the galaxy toolshed link that Eric sent out), as well as having individual plugins exist under the GMOD account that are “more official” (similar to an approved Galaxy IUC plugin) might be good, but not necessary.   
It's less that things are "more official" and more that "there is a group of volunteers who care about these things who are willing to update each other's stuff".

Nathan

On Jul 15, 2016, at 11:06 AM, Scott Cain <[hidden email]> wrote:

Hi Eric,

Do you have any interest in having a jbrowse-plugins repo in GMOD's github account?  It seems like having a place to put them is a good idea, but I'm good with the decentralized way it is now too.

I can't think of any downsides, but there probably are and they just haven't occurred to me.

Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
- Andrew Wilkey

T: +1-515-203-3774
E: [hidden email]
O: 0023 CGIL


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev


_______________________________________________
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--

Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
<a href="tel:404-692-2048">404-692-2048
[hidden email]
Not responding quickly enough?

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

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Re: jbrowse-plugins repo?

AWilkey
I actually fully agree. MEAN is *complete* overkill for most of this, was only done because I wanted to play with a few things on my own time. Honestly the actual frontend stuff is just angular looking for a JSON file, that happens in this case to pull from a mongodb instance. It could be from anywhere as long as it meets the requirements. The only thing that would need to really be revisited is the interface to add a plugin to the pending authorization list, which would be just as easy to do via appending to a JSON file in other ways.

On Fri, Jul 15, 2016 at 3:48 PM, Eric Rasche <[hidden email]> wrote:


On 15. juli 2016 20:35, Andrew Wilkey wrote:
The source is available here, actually, if not exactly perfect yet (threw the thing together over a weekend before the galaxy community conference as an excuse to play with deploying a full MEAN stack and to play with angular)

https://github.com/awilkey/pluginapp

That being said, there are plans afoot to add user auth and possibly to make a stand-alone local version that  can be put in a jbrowse directory and grab selected plugins via bower.


On Fri, Jul 15, 2016 at 3:29 PM, Nathan Dunn <[hidden email]> wrote:

On Jul 15, 2016, at 12:56 PM, Scott Cain <[hidden email][hidden email]> wrote:

I mostly want people to be able to find plugins.  Andrew Wilkey created a directory:


which seems like a step in the right direction.  A toolshed seems nice too, as long as somebody sets it up.
Toolshed == plugin directory, you shouldn't reuse the galaxy toolshed for anything other than galaxy (it's just not suited to it, it's too Galaxy specific).
 

This is very nice (thank you Andrew!).   I think the only difference would be putting the site source on github and managing the site as another github/GMOD project, but I think the overall theme is great.    Allowing users to register, login, edit, their entries, etc. would be ideal. 
Andrew has done great work on this, but I think if GMOD really want a plugin repository, they should really, strongly consider whether they needs such infrastructure as a MEAN stack. I would provide the counterpoint here of a number of galaxy related repositories which simply have a TSV file listing plugins/datasets/etc. Because your choices are:
  • Run a plugin service
    • Must implement auth, updating plugins, user management logic
    • Travis integration is not trivial if you (e.g.) wanted to make sure plugins were passing some tests
    • Editing entries requires (already implemented) logic for managing things in a database
    • Deployment is manual
    • Must handle service costs (human time deploying, updating, managing OS updates, etc)
  • Stick a TSV file in github
    • Registration/login is done by GH
    • Travis integration is trivial, we can run checks on every plugin regularly.
    • Editing entries is done via pull request and a couple of community moderators
    • Deployment is handled by GH pages, automatically, by clicking a button in the repo config.
    • Free

Galaxy IUC members tend to follow YAGNI pretty seriously, we've replaced a number of what would be traditional database by static sites. We've found that they're far easier to deal with. Need an API? Dump json files in a directory. No URL routing logic needed. No compute power needed.


In addition, it would be nice for developers to have a place to put them if they didn't know where else to put them.  I'm not convinced that it should necessarily be one plugin--one repo, but I can see the instinct that points that way.  The GBrowse data adaptors repo (GBrowse-adaptors) has multiple adaptors in it (3 or 4) but then, those are only maintained by Lincoln and me.
One-plugin per repo has the advantage of being bower installable and that's really, really useful.

Monorepo makes maintenance easier (community volunteers who are updating plugins can update all at once), but at the cost of writing your own plugin manager.

I’d like the option to install the plugins via bower (or a similar package manager) if desired at some point so that a user could easily switch branches, versions, repos, etc. with minimal work.   Its kind of what we’re hacking in now on top of JBrowse and it works okay.  

Nathan


On Fri, Jul 15, 2016 at 3:41 PM, Nathan Dunn <[hidden email]> wrote:

I just wanted to clarify if you were wanting to create a single repos for all of the plugins?  

I think we need the model of having a single repo per plugin (but talk me out of it).   Having something centralized that points back to the originating (likely decentralized) repos is good (similar to the galaxy toolshed link that Eric sent out), as well as having individual plugins exist under the GMOD account that are “more official” (similar to an approved Galaxy IUC plugin) might be good, but not necessary.   
It's less that things are "more official" and more that "there is a group of volunteers who care about these things who are willing to update each other's stuff".


Nathan

On Jul 15, 2016, at 11:06 AM, Scott Cain <[hidden email][hidden email]> wrote:

Hi Eric,

Do you have any interest in having a jbrowse-plugins repo in GMOD's github account?  It seems like having a place to put them is a good idea, but I'm good with the decentralized way it is now too.

I can't think of any downsides, but there probably are and they just haven't occurred to me.

Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
- Andrew Wilkey

T: <a href="tel:%2B1-515-203-3774" value="+15152033774" target="_blank">+1-515-203-3774
E: [hidden email][hidden email]
O: 0023 CGIL


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev


_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

--

Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
<a href="tel:404-692-2048" target="_blank">404-692-2048
[hidden email]
Not responding quickly enough?



--
- Andrew Wilkey

T: +1-515-203-3774
E: [hidden email]
O: 0023 CGIL

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
Gmod-ajax mailing list
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Re: jbrowse-plugins repo?

Eric Yao
I do like the idea of a monorepo and it's simplicity.   
However, I think I lean to developers managing their own repos.  More up-front implementation, yes.  
Self-publish.
The dockerhub seems to be a nice amalgam.  Individual github repos with a travis-like build/test.

Other thoughts.  Since, JBrowse is a visual tool, I'd like to see a BioJS-like registry front-end.  (of course, not all plugins are visual).
I also find it useful to see download counts and ratings.
We'd also like to eventually autoinstall, but this also implies packaging requirements need to be tighter.

Thanks Andrew, much appreciated that you've given this a real start.


On Fri, Jul 15, 2016 at 1:55 PM, Andrew Wilkey <[hidden email]> wrote:
I actually fully agree. MEAN is *complete* overkill for most of this, was only done because I wanted to play with a few things on my own time. Honestly the actual frontend stuff is just angular looking for a JSON file, that happens in this case to pull from a mongodb instance. It could be from anywhere as long as it meets the requirements. The only thing that would need to really be revisited is the interface to add a plugin to the pending authorization list, which would be just as easy to do via appending to a JSON file in other ways.

On Fri, Jul 15, 2016 at 3:48 PM, Eric Rasche <[hidden email]> wrote:


On 15. juli 2016 20:35, Andrew Wilkey wrote:
The source is available here, actually, if not exactly perfect yet (threw the thing together over a weekend before the galaxy community conference as an excuse to play with deploying a full MEAN stack and to play with angular)

https://github.com/awilkey/pluginapp

That being said, there are plans afoot to add user auth and possibly to make a stand-alone local version that  can be put in a jbrowse directory and grab selected plugins via bower.


On Fri, Jul 15, 2016 at 3:29 PM, Nathan Dunn <[hidden email]> wrote:

On Jul 15, 2016, at 12:56 PM, Scott Cain <[hidden email][hidden email]> wrote:

I mostly want people to be able to find plugins.  Andrew Wilkey created a directory:


which seems like a step in the right direction.  A toolshed seems nice too, as long as somebody sets it up.
Toolshed == plugin directory, you shouldn't reuse the galaxy toolshed for anything other than galaxy (it's just not suited to it, it's too Galaxy specific).
 

This is very nice (thank you Andrew!).   I think the only difference would be putting the site source on github and managing the site as another github/GMOD project, but I think the overall theme is great.    Allowing users to register, login, edit, their entries, etc. would be ideal. 
Andrew has done great work on this, but I think if GMOD really want a plugin repository, they should really, strongly consider whether they needs such infrastructure as a MEAN stack. I would provide the counterpoint here of a number of galaxy related repositories which simply have a TSV file listing plugins/datasets/etc. Because your choices are:
  • Run a plugin service
    • Must implement auth, updating plugins, user management logic
    • Travis integration is not trivial if you (e.g.) wanted to make sure plugins were passing some tests
    • Editing entries requires (already implemented) logic for managing things in a database
    • Deployment is manual
    • Must handle service costs (human time deploying, updating, managing OS updates, etc)
  • Stick a TSV file in github
    • Registration/login is done by GH
    • Travis integration is trivial, we can run checks on every plugin regularly.
    • Editing entries is done via pull request and a couple of community moderators
    • Deployment is handled by GH pages, automatically, by clicking a button in the repo config.
    • Free

Galaxy IUC members tend to follow YAGNI pretty seriously, we've replaced a number of what would be traditional database by static sites. We've found that they're far easier to deal with. Need an API? Dump json files in a directory. No URL routing logic needed. No compute power needed.


In addition, it would be nice for developers to have a place to put them if they didn't know where else to put them.  I'm not convinced that it should necessarily be one plugin--one repo, but I can see the instinct that points that way.  The GBrowse data adaptors repo (GBrowse-adaptors) has multiple adaptors in it (3 or 4) but then, those are only maintained by Lincoln and me.
One-plugin per repo has the advantage of being bower installable and that's really, really useful.

Monorepo makes maintenance easier (community volunteers who are updating plugins can update all at once), but at the cost of writing your own plugin manager.

I’d like the option to install the plugins via bower (or a similar package manager) if desired at some point so that a user could easily switch branches, versions, repos, etc. with minimal work.   Its kind of what we’re hacking in now on top of JBrowse and it works okay.  

Nathan


On Fri, Jul 15, 2016 at 3:41 PM, Nathan Dunn <[hidden email]> wrote:

I just wanted to clarify if you were wanting to create a single repos for all of the plugins?  

I think we need the model of having a single repo per plugin (but talk me out of it).   Having something centralized that points back to the originating (likely decentralized) repos is good (similar to the galaxy toolshed link that Eric sent out), as well as having individual plugins exist under the GMOD account that are “more official” (similar to an approved Galaxy IUC plugin) might be good, but not necessary.   
It's less that things are "more official" and more that "there is a group of volunteers who care about these things who are willing to update each other's stuff".


Nathan

On Jul 15, 2016, at 11:06 AM, Scott Cain <[hidden email][hidden email]> wrote:

Hi Eric,

Do you have any interest in having a jbrowse-plugins repo in GMOD's github account?  It seems like having a place to put them is a good idea, but I'm good with the decentralized way it is now too.

I can't think of any downsides, but there probably are and they just haven't occurred to me.

Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
- Andrew Wilkey

T: <a href="tel:%2B1-515-203-3774" value="+15152033774" target="_blank">+1-515-203-3774
E: [hidden email][hidden email]
O: 0023 CGIL


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev


_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

--

Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
<a href="tel:404-692-2048" target="_blank">404-692-2048
[hidden email]
Not responding quickly enough?



--
- Andrew Wilkey

T: <a href="tel:%2B1-515-203-3774" value="+15152033774" target="_blank">+1-515-203-3774
E: [hidden email]
O: 0023 CGIL

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
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Re: jbrowse-plugins repo?

nathandunn
I think the rich front end with a github data  backend (authenticated, versioned, atomic, flexible) that Eric proposed might be ideal given limited resources.  

Nathan

On Jul 15, 2016, at 3:14 PM, Eric Yao <[hidden email]> wrote:

I do like the idea of a monorepo and it's simplicity.   
However, I think I lean to developers managing their own repos.  More up-front implementation, yes.  
Self-publish.
The dockerhub seems to be a nice amalgam.  Individual github repos with a travis-like build/test.

Other thoughts.  Since, JBrowse is a visual tool, I'd like to see a BioJS-like registry front-end.  (of course, not all plugins are visual).
I also find it useful to see download counts and ratings.
We'd also like to eventually autoinstall, but this also implies packaging requirements need to be tighter.

Thanks Andrew, much appreciated that you've given this a real start.


On Fri, Jul 15, 2016 at 1:55 PM, Andrew Wilkey <[hidden email]> wrote:
I actually fully agree. MEAN is *complete* overkill for most of this, was only done because I wanted to play with a few things on my own time. Honestly the actual frontend stuff is just angular looking for a JSON file, that happens in this case to pull from a mongodb instance. It could be from anywhere as long as it meets the requirements. The only thing that would need to really be revisited is the interface to add a plugin to the pending authorization list, which would be just as easy to do via appending to a JSON file in other ways.

On Fri, Jul 15, 2016 at 3:48 PM, Eric Rasche <[hidden email]> wrote:


On 15. juli 2016 20:35, Andrew Wilkey wrote:
The source is available here, actually, if not exactly perfect yet (threw the thing together over a weekend before the galaxy community conference as an excuse to play with deploying a full MEAN stack and to play with angular)

https://github.com/awilkey/pluginapp

That being said, there are plans afoot to add user auth and possibly to make a stand-alone local version that  can be put in a jbrowse directory and grab selected plugins via bower.


On Fri, Jul 15, 2016 at 3:29 PM, Nathan Dunn <[hidden email]> wrote:

On Jul 15, 2016, at 12:56 PM, Scott Cain <[hidden email][hidden email]> wrote:

I mostly want people to be able to find plugins.  Andrew Wilkey created a directory:


which seems like a step in the right direction.  A toolshed seems nice too, as long as somebody sets it up.
Toolshed == plugin directory, you shouldn't reuse the galaxy toolshed for anything other than galaxy (it's just not suited to it, it's too Galaxy specific).
 

This is very nice (thank you Andrew!).   I think the only difference would be putting the site source on github and managing the site as another github/GMOD project, but I think the overall theme is great.    Allowing users to register, login, edit, their entries, etc. would be ideal. 
Andrew has done great work on this, but I think if GMOD really want a plugin repository, they should really, strongly consider whether they needs such infrastructure as a MEAN stack. I would provide the counterpoint here of a number of galaxy related repositories which simply have a TSV file listing plugins/datasets/etc. Because your choices are:
  • Run a plugin service
    • Must implement auth, updating plugins, user management logic
    • Travis integration is not trivial if you (e.g.) wanted to make sure plugins were passing some tests
    • Editing entries requires (already implemented) logic for managing things in a database
    • Deployment is manual
    • Must handle service costs (human time deploying, updating, managing OS updates, etc)
  • Stick a TSV file in github
    • Registration/login is done by GH
    • Travis integration is trivial, we can run checks on every plugin regularly.
    • Editing entries is done via pull request and a couple of community moderators
    • Deployment is handled by GH pages, automatically, by clicking a button in the repo config.
    • Free

Galaxy IUC members tend to follow YAGNI pretty seriously, we've replaced a number of what would be traditional database by static sites. We've found that they're far easier to deal with. Need an API? Dump json files in a directory. No URL routing logic needed. No compute power needed.


In addition, it would be nice for developers to have a place to put them if they didn't know where else to put them.  I'm not convinced that it should necessarily be one plugin--one repo, but I can see the instinct that points that way.  The GBrowse data adaptors repo (GBrowse-adaptors) has multiple adaptors in it (3 or 4) but then, those are only maintained by Lincoln and me.
One-plugin per repo has the advantage of being bower installable and that's really, really useful.

Monorepo makes maintenance easier (community volunteers who are updating plugins can update all at once), but at the cost of writing your own plugin manager.

I’d like the option to install the plugins via bower (or a similar package manager) if desired at some point so that a user could easily switch branches, versions, repos, etc. with minimal work.   Its kind of what we’re hacking in now on top of JBrowse and it works okay.  

Nathan


On Fri, Jul 15, 2016 at 3:41 PM, Nathan Dunn <[hidden email]> wrote:

I just wanted to clarify if you were wanting to create a single repos for all of the plugins?  

I think we need the model of having a single repo per plugin (but talk me out of it).   Having something centralized that points back to the originating (likely decentralized) repos is good (similar to the galaxy toolshed link that Eric sent out), as well as having individual plugins exist under the GMOD account that are “more official” (similar to an approved Galaxy IUC plugin) might be good, but not necessary.   
It's less that things are "more official" and more that "there is a group of volunteers who care about these things who are willing to update each other's stuff".


Nathan

On Jul 15, 2016, at 11:06 AM, Scott Cain <[hidden email][hidden email]> wrote:

Hi Eric,

Do you have any interest in having a jbrowse-plugins repo in GMOD's github account?  It seems like having a place to put them is a good idea, but I'm good with the decentralized way it is now too.

I can't think of any downsides, but there probably are and they just haven't occurred to me.

Scott


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