Re: [galaxy-dev] Galaxy December 20, 2012 Distribution & News Brief

2012-12-22 Thread Dannon Baker 
The toolshed dependency installation capabilities will fill this exact role -- 
for examples see how the blast+ suite or some of the other tools already 
migrated out of the codebase have been configured.  When you install these 
repositories from the toolshed you have the option to automatically download, 
build, and install dependencies along with the wrappers.


On Dec 22, 2012, at 9:19 AM, Scooter Willis  wrote:

> Hoping for the ease of apt-get for installing the binaries. Would be great
> if you could make that a requirement for installing specific version of
> binaries that align with the XML mapping in Galaxy. Would go a long way to
> make this easy and at the same time minimize the support requirements on
> why something is not working.
> 
> On 12/22/12 9:11 AM, "Dannon Baker"  wrote:
> 
>> The cloud automated update (through the admin UI) won't pull updated any
>> updated binaries -- that's up to you just like for a local install, and
>> you could still do it by ssh'ing in.  It will update all galaxy tool
>> wrappers (the .xml) that come with the distribution, but that's not the
>> binary version (which I think you're asking about, correct me if I'm
>> wrong).
>> 
>> And, the next release will probably be in early-mid January.
>> 
>> 
>> On Dec 22, 2012, at 9:07 AM, Scooter Willis  wrote:
>> 
>>> If I do the update will that also pull the latest versions of TopHat2
>>> and
>>> Bowtie2 as an example or just the Galaxy software?
>>> 
>>> Any guess on when the next distribution will release occur?
>>> 
>>> On 12/22/12 9:04 AM, "Dannon Baker"  wrote:
>>> 
 No -- we're reorganizing the storage approach the cloud uses and will
 not
 be updating for this distribution release.  Updates to the cloud
 deployment will most likely resume with the next distribution.
 
 Until then, you can always update your individual cloud instances to
 any
 revision you'd like.
 
 
 On Dec 22, 2012, at 8:59 AM, Scooter Willis 
 wrote:
 
> Is the cloud man Amazon EC2 instance updated with the latest?
> 
> From: Jennifer Jackson 
> Date: Thursday, December 20, 2012 8:49 PM
> To: Galaxy Announce , Galaxy User
> , Galaxy Dev 
> Subject: [galaxy-dev] Galaxy December 20, 2012 Distribution & News
> Brief
> 
> Galaxy Dec 20, 2012 Distribution & News Brief
> 
> Complete News Brief
> Highlights:
>   € Required Metadata Reset for instances running Tool Shed
> repositories. Be sure to learn how.
>   € Simplified tool config: all tools (including tool shed repos) can
> now have handlers and runners assigned based on their "short id".
>   € New GFF/GFF3 annotation support for Cuffcompare/merge/diff.
>   € More Updated tools: TopHat2, Bowtie2.
>   € Multiple pull-requests contributed by community (thanks!): #83,
> #85,
> #90, #91.
>   € Issue tracking help is now covered in detailed in our new wiki:
> Using the Galaxy Issue Board
>   € GCC2013 Training Day Topic Nominations are now open through January
> 11th
>   € Plus more Tool Shed updates, Bug Fixes, and improvements to
> Trackster, UI, Libraries, and Histories.
> 
> getgalaxy.org
> bitbucket.org/galaxy/galaxy-dist
> galaxy-dist.readthedocs.org
> 
> 
> new: $ hg clone http://www.bx.psu.edu/hg/galaxy
> galaxy-dist
> 
> upgrade: $ hg pull -u -r 36ad8aa7b922
> 
> 
> Best wishes for a safe and happy holiday,
> The Galaxy Team
> -- 
> Jennifer Jackson
> 
> http://galaxyproject.org
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> 
> http://lists.bx.psu.edu/
 
>>> 
>> 
> 


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Re: [galaxy-dev] Galaxy December 20, 2012 Distribution & News Brief

2012-12-22 Thread Scooter Willis 
Hoping for the ease of apt-get for installing the binaries. Would be great
if you could make that a requirement for installing specific version of
binaries that align with the XML mapping in Galaxy. Would go a long way to
make this easy and at the same time minimize the support requirements on
why something is not working.

On 12/22/12 9:11 AM, "Dannon Baker"  wrote:

>The cloud automated update (through the admin UI) won't pull updated any
>updated binaries -- that's up to you just like for a local install, and
>you could still do it by ssh'ing in.  It will update all galaxy tool
>wrappers (the .xml) that come with the distribution, but that's not the
>binary version (which I think you're asking about, correct me if I'm
>wrong).
>
>And, the next release will probably be in early-mid January.
>
>
>On Dec 22, 2012, at 9:07 AM, Scooter Willis  wrote:
>
>> If I do the update will that also pull the latest versions of TopHat2
>>and
>> Bowtie2 as an example or just the Galaxy software?
>> 
>> Any guess on when the next distribution will release occur?
>> 
>> On 12/22/12 9:04 AM, "Dannon Baker"  wrote:
>> 
>>> No -- we're reorganizing the storage approach the cloud uses and will
>>>not
>>> be updating for this distribution release.  Updates to the cloud
>>> deployment will most likely resume with the next distribution.
>>> 
>>> Until then, you can always update your individual cloud instances to
>>>any
>>> revision you'd like.
>>> 
>>> 
>>> On Dec 22, 2012, at 8:59 AM, Scooter Willis 
>>>wrote:
>>> 
 Is the cloud man Amazon EC2 instance updated with the latest?
 
 From: Jennifer Jackson 
 Date: Thursday, December 20, 2012 8:49 PM
 To: Galaxy Announce , Galaxy User
 , Galaxy Dev 
 Subject: [galaxy-dev] Galaxy December 20, 2012 Distribution & News
Brief
 
 Galaxy Dec 20, 2012 Distribution & News Brief
 
 Complete News Brief
 Highlights:
€ Required Metadata Reset for instances running Tool Shed
 repositories. Be sure to learn how.
€ Simplified tool config: all tools (including tool shed repos) can
 now have handlers and runners assigned based on their "short id".
€ New GFF/GFF3 annotation support for Cuffcompare/merge/diff.
€ More Updated tools: TopHat2, Bowtie2.
€ Multiple pull-requests contributed by community (thanks!): #83,
#85,
 #90, #91.
€ Issue tracking help is now covered in detailed in our new wiki:
 Using the Galaxy Issue Board
€ GCC2013 Training Day Topic Nominations are now open through January
 11th
€ Plus more Tool Shed updates, Bug Fixes, and improvements to
 Trackster, UI, Libraries, and Histories.
 
 getgalaxy.org
 bitbucket.org/galaxy/galaxy-dist
 galaxy-dist.readthedocs.org
 
 
 new: $ hg clone http://www.bx.psu.edu/hg/galaxy
 galaxy-dist
 
 upgrade: $ hg pull -u -r 36ad8aa7b922
 
 
 Best wishes for a safe and happy holiday,
 The Galaxy Team
 -- 
 Jennifer Jackson
 
 http://galaxyproject.org
 ___
 Please keep all replies on the list by using "reply all"
 in your mail client.  To manage your subscriptions to this
 and other Galaxy lists, please use the interface at:
 
 http://lists.bx.psu.edu/
>>> 
>> 
>


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Re: [galaxy-dev] Galaxy December 20, 2012 Distribution & News Brief

2012-12-22 Thread Dannon Baker 
The cloud automated update (through the admin UI) won't pull updated any 
updated binaries -- that's up to you just like for a local install, and you 
could still do it by ssh'ing in.  It will update all galaxy tool wrappers (the 
.xml) that come with the distribution, but that's not the binary version (which 
I think you're asking about, correct me if I'm wrong).

And, the next release will probably be in early-mid January.


On Dec 22, 2012, at 9:07 AM, Scooter Willis  wrote:

> If I do the update will that also pull the latest versions of TopHat2 and
> Bowtie2 as an example or just the Galaxy software?
> 
> Any guess on when the next distribution will release occur?
> 
> On 12/22/12 9:04 AM, "Dannon Baker"  wrote:
> 
>> No -- we're reorganizing the storage approach the cloud uses and will not
>> be updating for this distribution release.  Updates to the cloud
>> deployment will most likely resume with the next distribution.
>> 
>> Until then, you can always update your individual cloud instances to any
>> revision you'd like.
>> 
>> 
>> On Dec 22, 2012, at 8:59 AM, Scooter Willis  wrote:
>> 
>>> Is the cloud man Amazon EC2 instance updated with the latest?
>>> 
>>> From: Jennifer Jackson 
>>> Date: Thursday, December 20, 2012 8:49 PM
>>> To: Galaxy Announce , Galaxy User
>>> , Galaxy Dev 
>>> Subject: [galaxy-dev] Galaxy December 20, 2012 Distribution & News Brief
>>> 
>>> Galaxy Dec 20, 2012 Distribution & News Brief
>>> 
>>> Complete News Brief
>>> Highlights:
>>> € Required Metadata Reset for instances running Tool Shed
>>> repositories. Be sure to learn how.
>>> € Simplified tool config: all tools (including tool shed repos) can
>>> now have handlers and runners assigned based on their "short id".
>>> € New GFF/GFF3 annotation support for Cuffcompare/merge/diff.
>>> € More Updated tools: TopHat2, Bowtie2.
>>> € Multiple pull-requests contributed by community (thanks!): #83, #85,
>>> #90, #91.
>>> € Issue tracking help is now covered in detailed in our new wiki:
>>> Using the Galaxy Issue Board
>>> € GCC2013 Training Day Topic Nominations are now open through January
>>> 11th
>>> € Plus more Tool Shed updates, Bug Fixes, and improvements to
>>> Trackster, UI, Libraries, and Histories.
>>> 
>>> getgalaxy.org
>>> bitbucket.org/galaxy/galaxy-dist
>>> galaxy-dist.readthedocs.org
>>> 
>>> 
>>> new: $ hg clone http://www.bx.psu.edu/hg/galaxy
>>> galaxy-dist
>>> 
>>> upgrade: $ hg pull -u -r 36ad8aa7b922
>>> 
>>> 
>>> Best wishes for a safe and happy holiday,
>>> The Galaxy Team
>>> -- 
>>> Jennifer Jackson
>>> 
>>> http://galaxyproject.org
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>> 
>>> http://lists.bx.psu.edu/
>> 
> 


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Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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Re: [galaxy-dev] Galaxy December 20, 2012 Distribution & News Brief

2012-12-22 Thread Scooter Willis 
If I do the update will that also pull the latest versions of TopHat2 and
Bowtie2 as an example or just the Galaxy software?

Any guess on when the next distribution will release occur?

On 12/22/12 9:04 AM, "Dannon Baker"  wrote:

>No -- we're reorganizing the storage approach the cloud uses and will not
>be updating for this distribution release.  Updates to the cloud
>deployment will most likely resume with the next distribution.
>
>Until then, you can always update your individual cloud instances to any
>revision you'd like.
>
>
>On Dec 22, 2012, at 8:59 AM, Scooter Willis  wrote:
>
>> Is the cloud man Amazon EC2 instance updated with the latest?
>> 
>> From: Jennifer Jackson 
>> Date: Thursday, December 20, 2012 8:49 PM
>> To: Galaxy Announce , Galaxy User
>>, Galaxy Dev 
>> Subject: [galaxy-dev] Galaxy December 20, 2012 Distribution & News Brief
>> 
>> Galaxy Dec 20, 2012 Distribution & News Brief
>> 
>> Complete News Brief
>> Highlights:
>>  € Required Metadata Reset for instances running Tool Shed
>>repositories. Be sure to learn how.
>>  € Simplified tool config: all tools (including tool shed repos) can
>>now have handlers and runners assigned based on their "short id".
>>  € New GFF/GFF3 annotation support for Cuffcompare/merge/diff.
>>  € More Updated tools: TopHat2, Bowtie2.
>>  € Multiple pull-requests contributed by community (thanks!): #83, #85,
>>#90, #91.
>>  € Issue tracking help is now covered in detailed in our new wiki:
>>Using the Galaxy Issue Board
>>  € GCC2013 Training Day Topic Nominations are now open through January
>>11th
>>  € Plus more Tool Shed updates, Bug Fixes, and improvements to
>>Trackster, UI, Libraries, and Histories.
>> 
>> getgalaxy.org
>> bitbucket.org/galaxy/galaxy-dist
>> galaxy-dist.readthedocs.org
>>  
>> 
>> new: $ hg clone http://www.bx.psu.edu/hg/galaxy
>>  galaxy-dist
>> 
>> upgrade: $ hg pull -u -r 36ad8aa7b922
>> 
>> 
>> Best wishes for a safe and happy holiday,
>> The Galaxy Team
>> -- 
>> Jennifer Jackson
>> 
>> http://galaxyproject.org
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> 
>>  http://lists.bx.psu.edu/
>


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Galaxy December 20, 2012 Distribution & News Brief

2012-12-22 Thread Dannon Baker 
No -- we're reorganizing the storage approach the cloud uses and will not be 
updating for this distribution release.  Updates to the cloud deployment will 
most likely resume with the next distribution.

Until then, you can always update your individual cloud instances to any 
revision you'd like.


On Dec 22, 2012, at 8:59 AM, Scooter Willis  wrote:

> Is the cloud man Amazon EC2 instance updated with the latest?
> 
> From: Jennifer Jackson 
> Date: Thursday, December 20, 2012 8:49 PM
> To: Galaxy Announce , Galaxy User 
> , Galaxy Dev 
> Subject: [galaxy-dev] Galaxy December 20, 2012 Distribution & News Brief
> 
> Galaxy Dec 20, 2012 Distribution & News Brief
> 
> Complete News Brief
> Highlights:
>   • Required Metadata Reset for instances running Tool Shed repositories. 
> Be sure to learn how.
>   • Simplified tool config: all tools (including tool shed repos) can now 
> have handlers and runners assigned based on their "short id".
>   • New GFF/GFF3 annotation support for Cuffcompare/merge/diff.
>   • More Updated tools: TopHat2, Bowtie2.
>   • Multiple pull-requests contributed by community (thanks!): #83, #85, 
> #90, #91.
>   • Issue tracking help is now covered in detailed in our new wiki: Using 
> the Galaxy Issue Board
>   • GCC2013 Training Day Topic Nominations are now open through January 
> 11th
>   • Plus more Tool Shed updates, Bug Fixes, and improvements to 
> Trackster, UI, Libraries, and Histories.
> 
> getgalaxy.org
> bitbucket.org/galaxy/galaxy-dist
> galaxy-dist.readthedocs.org
>  
> 
> new: $ hg clone http://www.bx.psu.edu/hg/galaxy
>  galaxy-dist
> 
> upgrade: $ hg pull -u -r 36ad8aa7b922
> 
> 
> Best wishes for a safe and happy holiday,
> The Galaxy Team
> -- 
> Jennifer Jackson
> 
> http://galaxyproject.org
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> 
>  http://lists.bx.psu.edu/


___
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in your mail client.  To manage your subscriptions to this
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Re: [galaxy-dev] Galaxy December 20, 2012 Distribution & News Brief

2012-12-22 Thread Scooter Willis 
Is the cloud man Amazon EC2 instance updated with the latest?

From: Jennifer Jackson mailto:j...@bx.psu.edu>>
Date: Thursday, December 20, 2012 8:49 PM
To: Galaxy Announce 
mailto:galaxy-annou...@bx.psu.edu>>, Galaxy User 
mailto:galaxy-u...@bx.psu.edu>>, Galaxy Dev 
mailto:galaxy-...@bx.psu.edu>>
Subject: [galaxy-dev] Galaxy December 20, 2012 Distribution & News Brief

Galaxy Dec 20, 2012 Distribution & News 
Brief


Complete News Brief

Highlights:

 *   Required Metadata Reset for instances running Tool 
Shed repositories. Be sure to learn 
how.

 *   Simplified tool config: all tools (including tool shed repos) can now have 
handlers and runners assigned based on their "short id".

 *   New 
GFF/GFF3
 annotation support for 
Cuffcompare/merge/diff.

 *   More Updated tools: TopHat2, 
Bowtie2.

 *   Multiple pull-requests contributed by community (thanks!): 
#83,
 
#85,
 
#90,
 
#91.

 *   Issue tracking help is now covered in detailed in our new wiki: Using the 
Galaxy Issue Board

 *   GCC2013 Training Day Topic 
Nominations are now 
open through January 11th

 *   Plus more Tool Shed updates, 
Bug Fixes, and improvements to Trackster, UI, Libraries, and Histories.

getgalaxy.org

bitbucket.org/galaxy/galaxy-dist

galaxy-dist.readthedocs.org


new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: $ hg pull -u -r 36ad8aa7b922



Best wishes for a safe and happy holiday,

The Galaxy Team

--
Jennifer Jackson
http://galaxyproject.org
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