Galaxy December 20, 2012 Distribution & News Brief

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Galaxy December 20, 2012 Distribution & News Brief

Jen Hillman-Jackson

Complete News Brief

Highlights:


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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Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: Galaxy December 20, 2012 Distribution & News Brief

Scooter Willis-2
Is the cloud man Amazon EC2 instance updated with the latest?

From: Jennifer Jackson <[hidden email]>
Date: Thursday, December 20, 2012 8:49 PM
To: Galaxy Announce <[hidden email]>, Galaxy User <[hidden email]>, Galaxy Dev <[hidden email]>
Subject: [galaxy-dev] Galaxy December 20, 2012 Distribution & News Brief


Complete News Brief

Highlights:


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 December 20, 2012 Distribution & News Brief

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 <[hidden email]> wrote:

> Is the cloud man Amazon EC2 instance updated with the latest?
>
> From: Jennifer Jackson <[hidden email]>
> Date: Thursday, December 20, 2012 8:49 PM
> To: Galaxy Announce <[hidden email]>, Galaxy User <[hidden email]>, Galaxy Dev <[hidden email]>
> 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"
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and other Galaxy lists, please use the interface at:

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Re: Galaxy December 20, 2012 Distribution & News Brief

Scooter Willis-2
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" <[hidden email]> 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 <[hidden email]> wrote:
>
>> Is the cloud man Amazon EC2 instance updated with the latest?
>>
>> From: Jennifer Jackson <[hidden email]>
>> Date: Thursday, December 20, 2012 8:49 PM
>> To: Galaxy Announce <[hidden email]>, Galaxy User
>><[hidden email]>, Galaxy Dev <[hidden email]>
>> 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/
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Re: Galaxy December 20, 2012 Distribution & News Brief

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 <[hidden email]> 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" <[hidden email]> 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 <[hidden email]> wrote:
>>
>>> Is the cloud man Amazon EC2 instance updated with the latest?
>>>
>>> From: Jennifer Jackson <[hidden email]>
>>> Date: Thursday, December 20, 2012 8:49 PM
>>> To: Galaxy Announce <[hidden email]>, Galaxy User
>>> <[hidden email]>, Galaxy Dev <[hidden email]>
>>> 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 December 20, 2012 Distribution & News Brief

Scooter Willis-2
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" <[hidden email]> 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 <[hidden email]> 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" <[hidden email]> 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 <[hidden email]>
>>>wrote:
>>>
>>>> Is the cloud man Amazon EC2 instance updated with the latest?
>>>>
>>>> From: Jennifer Jackson <[hidden email]>
>>>> Date: Thursday, December 20, 2012 8:49 PM
>>>> To: Galaxy Announce <[hidden email]>, Galaxy User
>>>> <[hidden email]>, Galaxy Dev <[hidden email]>
>>>> 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/
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Re: Galaxy December 20, 2012 Distribution & News Brief

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 <[hidden email]> 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" <[hidden email]> 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 <[hidden email]> 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" <[hidden email]> 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 <[hidden email]>
>>>> wrote:
>>>>
>>>>> Is the cloud man Amazon EC2 instance updated with the latest?
>>>>>
>>>>> From: Jennifer Jackson <[hidden email]>
>>>>> Date: Thursday, December 20, 2012 8:49 PM
>>>>> To: Galaxy Announce <[hidden email]>, Galaxy User
>>>>> <[hidden email]>, Galaxy Dev <[hidden email]>
>>>>> 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/