Galaxy December 20, 2012 Distribution & News Brief
*Galaxy Dec 20, 2012 Distribution & News Brief <http://wiki.galaxyproject.org/News/2012_12_20_DistributionNewsBrief>* *Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2012_12_20>* *Highlights:* * *Required Metadata Reset* for instances running *Tool Shed <http://wiki.galaxyproject.org/Tool%20Shed>* repositories. Be sure to *learn how <http://wiki.galaxyproject.org/ResettingMetadataForInstalledRepositories>*. * *Simplified tool config*: all tools (including tool shed repos) can now have handlers and runners assigned based on their "short id". * *New* GFF <http://wiki.galaxyproject.org/Learn/Datatypes#GFF>/GFF3 <http://wiki.galaxyproject.org/Learn/Datatypes#GFF3> annotation support for *Cuffcompare/merge/diff <http://cufflinks.cbcb.umd.edu/manual.html>*. * *More Updated* tools: *TopHat2 <http://tophat.cbcb.umd.edu/manual.html>*, *Bowtie2 <http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml>*. * *Multiple pull-requests* contributed by community (thanks!): *#83 <https://bitbucket.org/galaxy/galaxy-central/pull-request/83/allow-a-datatypes-merge-method-to>*, *#85 <https://bitbucket.org/galaxy/galaxy-central/pull-request/85/another-round-of-bug-fixes-and>*, *#90 <https://bitbucket.org/galaxy/galaxy-central/pull-request/90/patch-to-make-extended_metadata-loader>*, *#91* <https://bitbucket.org/galaxy/galaxy-central/pull-request/91/fixing-missing-jobwrapper-import>. * *Issue tracking help* is now covered in detailed in our new wiki: *Using the Galaxy Issue Board <http://wiki.galaxyproject.org/Issues>* * *GCC2013 Training Day Topic Nominations <http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> are now open* through /*January 11th*/ <http://wiki.galaxyproject.org/Events/GCC2013/KeyDates> * *Plus* more *Tool Shed <http://wiki.galaxyproject.org/Tool%20Shed>* updates, *Bug Fixes*, and improvements to *Trackster, UI, Libraries, and Histories*. * getgalaxy.org <http://getgalaxy.org>* *bitbucket.org/galaxy/galaxy-dist <http://bitbucket.org/galaxy/galaxy-dist>* *galaxy-dist.readthedocs.org <http://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 <http://wiki.galaxyproject.org/Galaxy%20Team>*/ -- Jennifer Jackson http://galaxyproject.org
Is the cloud man Amazon EC2 instance updated with the latest? From: Jennifer Jackson <jen@bx.psu.edu<mailto:jen@bx.psu.edu>> Date: Thursday, December 20, 2012 8:49 PM To: Galaxy Announce <galaxy-announce@bx.psu.edu<mailto:galaxy-announce@bx.psu.edu>>, Galaxy User <galaxy-user@bx.psu.edu<mailto:galaxy-user@bx.psu.edu>>, Galaxy Dev <galaxy-dev@bx.psu.edu<mailto:galaxy-dev@bx.psu.edu>> Subject: [galaxy-dev] Galaxy December 20, 2012 Distribution & News Brief Galaxy Dec 20, 2012 Distribution & News Brief<http://wiki.galaxyproject.org/News/2012_12_20_DistributionNewsBrief> Complete News Brief<http://wiki.galaxyproject.org/DevNewsBriefs/2012_12_20> Highlights: * Required Metadata Reset for instances running Tool Shed<http://wiki.galaxyproject.org/Tool%20Shed> repositories. Be sure to learn how<http://wiki.galaxyproject.org/ResettingMetadataForInstalledRepositories>. * Simplified tool config: all tools (including tool shed repos) can now have handlers and runners assigned based on their "short id". * New GFF<http://wiki.galaxyproject.org/Learn/Datatypes#GFF>/GFF3<http://wiki.galaxyproject.org/Learn/Datatypes#GFF3> annotation support for Cuffcompare/merge/diff<http://cufflinks.cbcb.umd.edu/manual.html>. * More Updated tools: TopHat2<http://tophat.cbcb.umd.edu/manual.html>, Bowtie2<http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml>. * Multiple pull-requests contributed by community (thanks!): #83<https://bitbucket.org/galaxy/galaxy-central/pull-request/83/allow-a-datatypes-merge-method-to>, #85<https://bitbucket.org/galaxy/galaxy-central/pull-request/85/another-round-of-bug-fixes-and>, #90<https://bitbucket.org/galaxy/galaxy-central/pull-request/90/patch-to-make-extended_metadata-loader>, #91<https://bitbucket.org/galaxy/galaxy-central/pull-request/91/fixing-missing-jobwrapper-import>. * Issue tracking help is now covered in detailed in our new wiki: Using the Galaxy Issue Board<http://wiki.galaxyproject.org/Issues> * GCC2013 Training Day Topic Nominations<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> are now open through January 11th<http://wiki.galaxyproject.org/Events/GCC2013/KeyDates> * Plus more Tool Shed<http://wiki.galaxyproject.org/Tool%20Shed> updates, Bug Fixes, and improvements to Trackster, UI, Libraries, and Histories. getgalaxy.org<http://getgalaxy.org> bitbucket.org/galaxy/galaxy-dist<http://bitbucket.org/galaxy/galaxy-dist> galaxy-dist.readthedocs.org<http://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<http://wiki.galaxyproject.org/Galaxy%20Team> -- Jennifer Jackson http://galaxyproject.org
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 <HWillis@scripps.edu> wrote:
Is the cloud man Amazon EC2 instance updated with the latest?
From: Jennifer Jackson <jen@bx.psu.edu> Date: Thursday, December 20, 2012 8:49 PM To: Galaxy Announce <galaxy-announce@bx.psu.edu>, Galaxy User <galaxy-user@bx.psu.edu>, Galaxy Dev <galaxy-dev@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 ___________________________________________________________ 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:
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" <dannonbaker@me.com> 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 <HWillis@scripps.edu> wrote:
Is the cloud man Amazon EC2 instance updated with the latest?
From: Jennifer Jackson <jen@bx.psu.edu> Date: Thursday, December 20, 2012 8:49 PM To: Galaxy Announce <galaxy-announce@bx.psu.edu>, Galaxy User <galaxy-user@bx.psu.edu>, Galaxy Dev <galaxy-dev@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 ___________________________________________________________ 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:
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 <HWillis@scripps.edu> 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" <dannonbaker@me.com> 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 <HWillis@scripps.edu> wrote:
Is the cloud man Amazon EC2 instance updated with the latest?
From: Jennifer Jackson <jen@bx.psu.edu> Date: Thursday, December 20, 2012 8:49 PM To: Galaxy Announce <galaxy-announce@bx.psu.edu>, Galaxy User <galaxy-user@bx.psu.edu>, Galaxy Dev <galaxy-dev@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 ___________________________________________________________ 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:
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" <dannonbaker@me.com> 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 <HWillis@scripps.edu> 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" <dannonbaker@me.com> 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 <HWillis@scripps.edu> wrote:
Is the cloud man Amazon EC2 instance updated with the latest?
From: Jennifer Jackson <jen@bx.psu.edu> Date: Thursday, December 20, 2012 8:49 PM To: Galaxy Announce <galaxy-announce@bx.psu.edu>, Galaxy User <galaxy-user@bx.psu.edu>, Galaxy Dev <galaxy-dev@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 ___________________________________________________________ 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:
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 <HWillis@scripps.edu> 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" <dannonbaker@me.com> 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 <HWillis@scripps.edu> 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" <dannonbaker@me.com> 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 <HWillis@scripps.edu> wrote:
Is the cloud man Amazon EC2 instance updated with the latest?
From: Jennifer Jackson <jen@bx.psu.edu> Date: Thursday, December 20, 2012 8:49 PM To: Galaxy Announce <galaxy-announce@bx.psu.edu>, Galaxy User <galaxy-user@bx.psu.edu>, Galaxy Dev <galaxy-dev@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 ___________________________________________________________ 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:
participants (3)
-
Dannon Baker -
Jennifer Jackson -
Scooter Willis