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Mid 2015 Galaxy CloudMan release
by Dave Clements 03 Sep '15

03 Sep '15

*We just released an update to Galaxy CloudMan.* CloudMan offers an easy way to get a personal and completely functional instance of Galaxy in the cloud in just a few minutes, without any manual configuration or imposed quotas. Once running, you have complete control over Galaxy, including the ability to install new tools. This is the most complete update of the Galaxy on the Cloud platform to date with all the cloud components being built from the ground up. The following is a summary of the major changes: - *Galaxy on the Cloud*: all new galaxy and indices file systems, with Galaxy 15.07 release, ~200 preinstalled Galaxy tools, and nearly half a terabyte of updated reference genome data. - *Galaxy on the Cloud*: switched to a different Cloud Launch application, available athttps://launch.usegalaxy.org/ - *Galaxy on the Cloud*: Integrated Galaxy IPython Interactive Environments - *CloudMan*: Creating cluster shares is now fast (~30 seconds vs. hours) - Created a wealth of new documentation, including a description of the all new automated method for building private/custom instances https://wiki.galaxyproject.org/CloudMan/Building See the CHANGELOG <https://github.com/galaxyproject/cloudman/blob/master/CHANGELOG.md> for a more complete set of changes or just give it a try: see the all new Getting Started <https://wiki.galaxyproject.org/CloudMan/GettingStarted> documentation. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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July 2015 Galaxy Release (v 15.07)
by Martin Čech 03 Sep '15

03 Sep '15

The very-slightly-delayed July 2015 Galaxy Release is out! Full release notes: http://galaxy.readthedocs.org/en/master/releases/15.07_announce.html Highlights * *Interactive Environments* - The interactive environments (IE) framework features several updates this release and Galaxy is now distributed with a new IE for RStudio implemented by Eric Rasche. * *Workflow Editor Enhancements* - The workflow editor has been significantly revamped - it now uses newer tool form components and allow construction of workflows with tools explicitly producing output collections. * *Policies for Committers and Pull Requests* - The process for adding committers to the project and fielding pull requests has been formalized and documented in the source code. Three new committers have been added to the project - Björn Grüning, Nicola Soranzo, and Eric Rasche. *Thank you for using Galaxy! * The Galaxy Team https://wiki.galaxyproject.org/GalaxyTeam

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September 2015 Galactic News
by Dave Clements 01 Sep '15

01 Sep '15

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Galaxy Tool Shed Security Vulnerability - Repository uploads
by Nate Coraor 13 Aug '15

13 Aug '15

*DESCRIPTION* A security vulnerability was recently discovered by Peter Cock at the James Hutton Institute that would allow a malicious actor to upload new versions to repositories on which they have not been granted access. *AFFECTED VERSIONS* This issue affects versions of the Tool Shed beginning with 15.01. Earlier versions are not affected. *IMPACT* Because the Tool Shed is used to install software in Galaxy, if exploited, the impact could result in arbitrary code execution on Galaxy servers if a malicious tool is uploaded to a previously trusted repository, and that compromised version is subsequently installed by a Galaxy administrator. As such, Tool Shed administrators are strongly encouraged to update immediately. *INSTRUCTIONS* To apply the fix, first identify your current Galaxy release version using the `git branch` or `hg branch` commands. If you are on a 'release_YY.MM' branch, you can update with: % git pull or: % hg pull -u The process above can also be used to update to the 15.07 release if you are on the 'master' git branch or the 'stable' hg branch. If you are on the 'master'/'stable' branch and wish to remain on your current Galaxy major release, check the 'lib/galaxy/version.py' file to determine your major release version, then update to the appropriate branch: % git checkout -b release_YY.MM origin/release_YY.MM % git pull or: % hg pull % hg update release_YY.MM For the changes to take effect, YOU MUST RESTART ALL TOOL SHED SERVER PROCESSES. On behalf of the Galaxy Committers, --nate

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Galaxy Security Vulnerability - Reflected XSS
by Nate Coraor 13 Aug '15

13 Aug '15

*DESCRIPTION* A security vulnerability was recently discovered by Scott B. Szakonyi at The Center for Research Computing at the University of Notre Dame that would allow a malicious actor to exploit the workflow import form to cause a user's browser to execute javascript not originating from within Galaxy. This could allow the malicious actor to gain unauthorized access to Galaxy accounts or client data. *AFFECTED VERSIONS* This issue affects all known versions of Galaxy. In early 2015, the Galaxy Team performed a large XSS audit, the results of which were applied to versions 14.10 and later. Using Galaxy versions earlier than 14.10 is not advisable. *IMPACT* Exploitation of reflected XSS vulnerabilities typically requires some coordination, but the consequences of exploitation can result in data or account exposure, so the risk of leaving the issue unfixed is moderate. Administrators of affected servers are encouraged to update immediately. *INSTRUCTIONS* To apply the fix, first identify your current Galaxy release version using the `git branch` or `hg branch` commands. If you are on a 'release_YY.MM' branch, you can update with: % git pull or: % hg pull -u The process above can also be used to update to the 15.07 release if you are on the 'master' git branch or the 'stable' hg branch. If you are on the 'master'/'stable' branch and wish to remain on your current Galaxy major release, check the 'lib/galaxy/version.py' file to determine your major release version, then update to the appropriate branch: % git checkout -b release_YY.MM origin/release_YY.MM % git pull or: % hg pull % hg update release_YY.MM For the changes to take effect, YOU MUST RESTART ALL GALAXY SERVER PROCESSES. On behalf of the Galaxy Committers, --nate

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Galaxy Security Vulnerability - Authentication framework with LDAP
by Nate Coraor 13 Aug '15

13 Aug '15

*DESCRIPTION* A security vulnerability was recently discovered by Nicola Soranzo at The Genome Analysis Centre that would allow unauthorized access to Galaxy accounts on Galaxy servers using the LDAP authentication framework plugin. This is due to the fact that LDAP may be configured to allow anonymous binds, and the LDAP plugin does not check that binding with the provided username/password was not anonymous. *AFFECTED VERSIONS* The authentication framework is a new feature as of the 15.05 Galaxy release, so earlier versions are not affected. In versions 15.05 and later, the LDAP plugin is not used by default, so only Galaxy servers which have been configured to use this new functionality are affected. Galaxy servers using upstream delegated authentication (where authentication is performed by the proxy server, e.g. Apache or nginx) are not affected. *IMPACT* Administrators of affected servers are STRONGLY encouraged to update immediately, as the vulnerability allows unauthorized access to Galaxy accounts. *INSTRUCTIONS* To apply the fix, first identify your current Galaxy release version using the `git branch` or `hg branch` commands. If you are on a 'release_YY.MM' branch, you can update with: % git pull or: % hg pull -u The process above can also be used to update to the 15.07 release if you are on the 'master' git branch or the 'stable' hg branch. If you are on the 'master'/'stable' branch and wish to remain on your current Galaxy major release, check the 'lib/galaxy/version.py' file to determine your major release version, then update to the appropriate branch: % git checkout -b release_YY.MM origin/release_YY.MM % git pull or: % hg pull % hg update release_YY.MM For the changes to take effect, YOU MUST RESTART ALL GALAXY SERVER PROCESSES. On behalf of the Galaxy Committers, --nate

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August 2015 Galactic News
by Dave Clements 31 Jul '15

31 Jul '15

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June 2015 Galaxy New
by Dave Clements 01 Jun '15

01 Jun '15

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May 2015 Galaxy Release (v 15.05)
by Jennifer Hillman-Jackson 15 May '15

15 May '15

*The May 2015 Galaxy Release is out!* Release Notes v 15.05 <http://galaxy.readthedocs.org/en/master/releases/15.05_announce.html> Release Highlights - *Authentication Plugins* - Galaxy now has native support for LDAP and Active Directory via a new community developed authentication plugin system. - *Tool Sections* - Tool parameters may now be groupped into collapsable sections. - *Collection Creators* - New widgets have been added that allow much more flexibility when creating simple dataset pair and list collections. - And *much more <http://galaxy.readthedocs.org/en/master/releases/15.05_announce.html>* The release notes have a new home at Read the Docs <http://galaxy.readthedocs.org/en/master/releases/15.05_announce.html>. We hope that you like the new format as much as we do! *Thanks for using Galaxy! * The Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- Registration for the 2015 Galaxy Community Conference is OPEN! http://gcc2015.tsl.ac.uk *Love* *Galaxy*? We are inviting Galaxy power end-users as well as scientists and bioinformatics support researchers to *join us for the inaugural* *Galaxy Data Wrangling Hackathon* preceding the 2015 Galaxy Community Conference conference this July. http://gcc2015.tsl.ac.uk/data-hackathon

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GCC2015: Early Reg closes 22 May; Call for Birds-of-a-feather; and more
by Dave Clements 14 May '15

14 May '15

Hello all, A couple of GCC2015 related items: *Early Registration closes 22 May* Just a reminder that early registration <http://gcc2015.tsl.ac.uk/registration/> for the 2015 Galaxy Community Conference (GCC2015, http://gcc2015.tsl.ac.uk/) closes Friday, 22 May. Registering after that costs an average of 40% more. Space is limited at several events, and when that space is gone, it's gone for good. Register now <http://gcc2015.tsl.ac.uk/registration/> and attend the events you want to, and save 40%. GCC2015 includes several new events and features even more training than before. *Call for Birds of a Feather (BoFs) Meetups* *Birds of a feather* meetups are informal gatherings of GCC attendees with a shared interest. They are an essential part of GCCs. If you have an idea then for a BoF then you are strongly encouraged to propose one: https://wiki.galaxyproject.org/Events/GCC2015/BoFs *Oral Presentation Abstracts are Online* *Most* of the abstracts for accepted talks at GCC2015 are now online. We expect to put a few more up in the coming week. http://gcc2015.tsl.ac.uk/abstracts/ They aren't (yet) listed in any particular order. Again, please do remember to register by 22 May, and we hope to see you in Norwich! Cheers, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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