Development News Brief

June 3, 2013

It is critical that you reset the metadata on your installed tool shed repositories when you upgrade your Galaxy instance to this revision!
New Tool Shed Features
- Resetting metadata on your repositories
Tool Shed feature enhancements
Miscellaneous Tool Shed fixes and enhancements
Accepted Tool Shed pull requests
Tool Shed Tickets

# Get Galaxy

Please note new upgrade syntax

	getgalaxy.org
	galaxy-dist.readthedocs.org
	bitbucket.org/galaxy/galaxy-dist

new:	`$ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable`
upgrade:	`$ hg pull` `$ hg update release_2013.06.03`

# Release Process

If you need a refresher about how to update or this is your first update in a while, please review the instructions at Get Galaxy. Even more details are in the prior News Brief.

# Python 2.5 Support Has Ended

As of this release, Galaxy no longer supports Python 2.5. More in the ticket: http://trello.com/c/OQT8Iun8

## Required metadata reset for installed tool shed repositories

It is critical that you reset the metadata on your installed tool shed repositories when you upgrade your Galaxy instance to this revision!

When a tool shed repository is installed into your local Galaxy instance, metadata is generated for the repository as a part of the installation process and stored in the tool_shed_repository.metadatatable column in the Galaxy database. This automatic process inspects the contents of the specific revision of the installed repository and generates and stores important information about it. This metadata information is used by certain Galaxy features. As new features are added to Galaxy or the tool shed, the process that generates this installed tool shed repository metadata within the Galaxy instance may be enhanced to accommodate information about the new features. Read more…

# Tool Shed

Tool Shed

New Tool Shed Features

Resetting metadata on your repositories

There may be occasions when the entire changelog should be inspected and all of the metadata reset on it. You can reset all metadata on a repository that you are authorized to change by selecting the Reset all repository metadata option from the Repository Actions menu. Sometimes it may be necessary to reset metadata on multiple repositories. For example, if metadata is changed for a repository that is a dependency of another repository, it may be necessary to reset all metadata on each of the repositories in the dependency chain. Read more…

Tool Shed feature enhancements

#1 Supported tags sets for the tool_dependencies.xml file Several new tags and attributes are supported for tool dependency definitions. These tags and attributes are supported when installing repositories with tool dependencies in either a browser or using the enhanced Galaxy API. Read more…
#2 The bells and whistles of tool dependency definitions In some cases, a dependency definition author may want to write a definition whose dependency package (e.g., osra) can require a previously compiled binary (e.g., graphicsmagick) during compilation as well as tool execution time when the tool is using the compiled [osra] binary. This is possible using a combination of three tool dependency definition tag sets, which must be defined in the tool_dependencies.xml file in the order discussed here. Read more…
#3 Framework enhancements that process repository_dependencies.xml files Several enhancements have been made to the Tool Shed framework that processes repository dependency definitions contained in a repository_dependencies.xml file in a repository. Both of the previously required "toolshed" and "changeset_revision" attributes are now optional, and a new tag attribute is supported for ordering the installation of repository dependencies. This new attribute named "prior_installation_required", and if set to True in the repository dependency definition for a certain repository XYZ, then Galaxy's repository installation process will ensure that the required repository (XYZ's defined repository dependency) is installed prior to the installation of XYZ. These enhancements are supported when installing repositories with repository dependencies in either a browser or using the enhanced Galaxy API. Read more…
#4 The automated tool test framework The Tool Shed includes an extensive installation and test framework that works with repositories that contain valid tools. It is designed to be executed by cron regularly and sends email notification to a mail list when each run is completed. The framework is very flexible. It can be executed automatically or manually on a single repository revision or all revisions of all repositories in the tool shed. Read more…
#5 The Tool Shed API The RESTful Tool Shed API has been significantly enhanced. Read more…
#6 Tool Shed Functional Test Framework Many additional tests have been added to the tool shed functional test framework. Read more…

Miscellaneous Tool Shed fixes and enhancements

Enhance the Repositories that contain tools with invalid functional tests grid to allow for sorting by repository owner. Enhance several of the repository review grids to enable sorting by repository owner.
Clean up the main repositories by category grid and add a tools verified column.
Raise exceptions when tool dependency definition <install> and <set_environment> tags define an unsupported version attribute.
Add more granular lists of writable repositories for the current user: repositories with missing tool test components, repositories with failing tool tests and repositories with no failing tool tests.
Move the My invalid tools menu item in the tool shed to a grid that filters to the latest metadata revision.
The "Repository Actions" menu has been standardized so that the menu is virtually the same on all pages.
Attempt to standardize the main page title for repository pages in the tool shed by displaying the repository name.
Enable dynamic configuration of message box content and visibility in the wsgi .ini file. Display the configured brand, if any, in the element.</li> <li>For tool dependencies whose installation ended in an error, still display them when attempting to uninstall them.</li> <li>Enhancements for the tool shed repository View changeset page: display the commit message, display both the ctx rev and the changeset hash in the title bar, and add Previous changeset and Next changeset buttons to allow for easier scrolling through the repository changelog.</li> <li>Fix for reinstalling an uninstalled repository when leaving the no changes checkbox checked and entering text into the new tool panel section field.</li> <li>Keep all contents (including comments) of dependency definition files when re-writing them to include missing toolshed and <code>changeset_revision</code> attributes.</li> <li>Eliminate the use of Galaxy's <code>elementree</code> egg within the tool shed.</li> </ol> <h3 id="accepted-tool-shed-pull-requests"><a href="#accepted-tool-shed-pull-requests" aria-hidden="true"><span class="icon icon-link"></span></a>Accepted Tool Shed pull requests</h3> <p>Support for Toolsheds with external auth enabled, pull request <strong><a href="https://bitbucket.org/galaxy/galaxy-central/pull-request/155" target="_blank" rel="noopener noreferrer">#155</a></strong>. Thanks to <a href="https://bitbucket.org/kiwiroy" target="_blank" rel="noopener noreferrer">Roy Storey</a>.</p> <h3 id="tool-shed-tickets"><a href="#tool-shed-tickets" aria-hidden="true"><span class="icon icon-link"></span></a>Tool Shed Tickets</h3> <table> <tr> <td> <a href='https://trello.com/c/49vjZrJy '>https://trello.com/c/49vjZrJy </a></td> <td> <a href='https://trello.com/c/zd0v8jHq '>https://trello.com/c/zd0v8jHq </a></td> <td> <a href='https://trello.com/c/20EykJrK '>https://trello.com/c/20EykJrK </a></td> <td> <a href='https://trello.com/c/G3MAzlEC '>https://trello.com/c/G3MAzlEC </a></td> </tr> <tr> <td> <a href='https://trello.com/c/9yERGRt8 '>https://trello.com/c/9yERGRt8 </a></td> <td> <a href='https://trello.com/c/wNdXNOGU '>https://trello.com/c/wNdXNOGU </a></td> <td> <a href='https://trello.com/c/ezExflJd '>https://trello.com/c/ezExflJd </a></td> <td> <a href='https://trello.com/c/iICpByzT '>https://trello.com/c/iICpByzT </a></td> </tr> <tr> <td> <a href='https://trello.com/c/IXJjuXTm '>https://trello.com/c/IXJjuXTm </a></td> <td> <a href='https://trello.com/c/Djda4lD0 '>https://trello.com/c/Djda4lD0 </a></td> <td> <a href='https://trello.com/c/hdV3C24u '>https://trello.com/c/hdV3C24u </a></td> <td> <a href='https://trello.com/c/Qi7QRgdT '>https://trello.com/c/Qi7QRgdT </a></td> </tr> <tr> <td> <a href='https://trello.com/c/45TRG5DY '>https://trello.com/c/45TRG5DY </a></td> <td> <a href='https://trello.com/c/0Cljlxt3 '>https://trello.com/c/0Cljlxt3 </a></td> <td> <a href='https://trello.com/c/KQd4j3lz '>https://trello.com/c/KQd4j3lz </a></td> <td> <a href='https://trello.com/c/mqigrjfr '>https://trello.com/c/mqigrjfr </a></td> </tr> <tr> <td> <a href='https://trello.com/c/QTeSmNSs '>https://trello.com/c/QTeSmNSs </a></td> <td> <a href='https://trello.com/c/O9YmzUT4 '>https://trello.com/c/O9YmzUT4 </a></td> <td> <a href='https://trello.com/c/71Bx8TcB '>https://trello.com/c/71Bx8TcB </a></td> <td> <a href='https://trello.com/c/2tkPpVkL '>https://trello.com/c/2tkPpVkL </a></td> </tr> <tr> <td> <a href='https://trello.com/c/0zvUBdJJ '>https://trello.com/c/0zvUBdJJ </a></td> <td> <a href='https://trello.com/c/HTJWRo3Z '>https://trello.com/c/HTJWRo3Z </a></td> <td> <a href='https://trello.com/c/AhNBPA8K '>https://trello.com/c/AhNBPA8K </a></td> <td> <a href='https://trello.com/c/hlYDzFQW '>https://trello.com/c/hlYDzFQW </a></td> </tr> <tr> <td> <a href='https://trello.com/c/hXNIbIMh '>https://trello.com/c/hXNIbIMh </a></td> <td> <a href='https://trello.com/c/ZDRQ6m3Y '>https://trello.com/c/ZDRQ6m3Y </a></td> <td> <a href='https://trello.com/c/17HndRkh '>https://trello.com/c/17HndRkh </a></td> <td> <a href='https://trello.com/c/QY0Z7L7p '>https://trello.com/c/QY0Z7L7p </a></td> </tr> <tr> <td> <a href='https://trello.com/c/ghUbjr8c '>https://trello.com/c/ghUbjr8c </a></td> <td> <a href='https://trello.com/c/iKiZytSf '>https://trello.com/c/iKiZytSf </a></td> <td> <a href='https://trello.com/c/awKBxrGy '>https://trello.com/c/awKBxrGy </a></td> <td> <a href='https://trello.com/c/noxRnGEv '>https://trello.com/c/noxRnGEv </a></td> </tr> <tr> <td> <a href='https://trello.com/c/ondndIfd '>https://trello.com/c/ondndIfd </a></td> <td> <a href='https://trello.com/c/3TGyWggI '>https://trello.com/c/3TGyWggI </a></td> <td> <a href='https://trello.com/c/zfQaURtr '>https://trello.com/c/zfQaURtr </a></td> <td> <a href='https://trello.com/c/MxgHVnT9 '>https://trello.com/c/MxgHVnT9 </a></td> </tr> <tr> <td> <a href='https://trello.com/c/ZoslAcBD '>https://trello.com/c/ZoslAcBD </a></td> <td> <a href='https://trello.com/c/dL8dGPYf '>https://trello.com/c/dL8dGPYf </a></td> <td> <a href='https://trello.com/c/YRsP3wpS '>https://trello.com/c/YRsP3wpS </a></td> <td> <a href='https://trello.com/c/wJN65GdV '>https://trello.com/c/wJN65GdV </a></td> </tr> <tr> <td> <a href='https://trello.com/c/wJN65GdV '>https://trello.com/c/wJN65GdV </a></td> <td> <a href='https://trello.com/c/dcT7qOfc '>https://trello.com/c/dcT7qOfc </a></td> <td> <a href='https://trello.com/c/SMdJQ5zn '>https://trello.com/c/SMdJQ5zn </a></td> </tr> </table> <br /> # Tools <ol> <li><code>GenomeSpace</code>: Update <code>serverurl.properties</code> file location to work around issue with jumbo frames. <a href="https://trello.com/c/7tZli0PH" target="_blank" rel="noopener noreferrer">https://trello.com/c/7tZli0PH</a></li> <li><em>MAF to BED</em> corrected to fix problem with false error states. <a href="https://trello.com/c/y55KbTRt" target="_blank" rel="noopener noreferrer">https://trello.com/c/y55KbTRt</a></li> <li><code>STDERR</code> and <code>STDOUT</code> will now show beginning and end of contents, instead of just the beginning, when truncated. <a href="https://trello.com/c/v31ECJPr" target="_blank" rel="noopener noreferrer">https://trello.com/c/v31ECJPr</a></li> <li>Fix displaying <code>STDERR</code> and <code>STDOUT</code> links in dataset info. <a href="https://trello.com/c/2ZTg6Tiq" target="_blank" rel="noopener noreferrer">https://trello.com/c/2ZTg6Tiq</a></li> <li>Auto Focus on first item on forms. <a href="https://trello.com/c/etlSFyEr" target="_blank" rel="noopener noreferrer">https://trello.com/c/etlSFyEr</a></li> <li>Clarify tool tip FASTQ Summary Statistics. <a href="https://trello.com/c/LX0ma0uQ" target="_blank" rel="noopener noreferrer">https://trello.com/c/LX0ma0uQ</a></li> <li>Resolve <code>BSD/GNU</code> grep version behavior differences. <a href="https://trello.com/c/dPUZ9zEA" target="_blank" rel="noopener noreferrer">https://trello.com/c/dPUZ9zEA</a></li> <li>Filter and Sort: "Select" tool, improved handling of special characters. <a href="https://trello.com/c/cwrBpNP9" target="_blank" rel="noopener noreferrer">https://trello.com/c/cwrBpNP9</a></li> <li>Change file-merging to use copy.copyfileobj() rather than cat and mv. <a href="https://trello.com/c%5B/Gaqoc6H8%5D(/archive/dev-news-briefs/2013-06-03/Gaqoc6H8/" target="_blank" rel="noopener noreferrer">https://trello.com/c[/Gaqoc6H8](/archive/dev-news-briefs/2013-06-03/Gaqoc6H8/</a>)</li> <li>Data Manager: Fix for detecting job error in data manager tools; needed as a result of recent job flow changes. <a href="https://trello.com/c%5B/EtXd4zqq%5D(/archive/dev-news-briefs/2013-06-03/EtXd4zqq/" target="_blank" rel="noopener noreferrer">https://trello.com/c[/EtXd4zqq](/archive/dev-news-briefs/2013-06-03/EtXd4zqq/</a>)</li> </ol> <br /> # Scatterplot <ol> <li>Enhancements to handlers, display, and data input parsing. <a href="https://trello.com/c/5jk3k7Td" target="_blank" rel="noopener noreferrer">https://trello.com/c/5jk3k7Td</a></li> </ol> <p><a href='/archive/dev-news-briefs/2013-06-03/'><div class="img-sizer" style="width: 500px"><img src="/images/news-graphics/2013_06_03_scatterplot-1.png" alt="scatterplot"></div></a></p> <br /> # Trackster <ol> <li>Composite track improvements. <a href="https://trello.com/c/hPcrKfJl" target="_blank" rel="noopener noreferrer">https://trello.com/c/hPcrKfJl</a></li> <li>Insert a button for Trackster Visualization into data display viewer. <a href="https://trello.com/c/KGNfWZEH" target="_blank" rel="noopener noreferrer">https://trello.com/c/KGNfWZEH</a></li> <li>Add Bigwig support for BAM coverage. <a href="https://trello.com/c/GV7nTlg9" target="_blank" rel="noopener noreferrer">https://trello.com/c/GV7nTlg9</a></li> <li>VCF visualization in trackster. <a href="https://trello.com/c/1dj3lTtU" target="_blank" rel="noopener noreferrer">https://trello.com/c/1dj3lTtU</a></li> </ol> <br /> # Histories & Datasets <ol> <li>Delete Hidden Datasets menu option. <a href="https://trello.com/c/0SoREcMn" target="_blank" rel="noopener noreferrer">https://trello.com/c/0SoREcMn</a></li> <li>When copying datasets to the current history always refresh history. <a href="https://trello.com/c/jY5HSdu1" target="_blank" rel="noopener noreferrer">https://trello.com/c/jY5HSdu1</a></li> </ol> <br /> # Libraries <ol> <li>Library API problem in galaxy-central default but not stable. <a href="https://trello.com/c/TbWP1tad" target="_blank" rel="noopener noreferrer">https://trello.com/c/TbWP1tad</a></li> </ol> <br /> # UI <ol> <li>Unicode fixes for previewing large datasets. <a href="https://trello.com/c/BHRKkcaw" target="_blank" rel="noopener noreferrer">https://trello.com/c/BHRKkcaw</a></li> <li>Unicode fixes for uploading by file in upload tool. <a href="https://trello.com/c%5B/O0M8W8X8%5D(/archive/dev-news-briefs/2013-06-03/O0M8W8X8/" target="_blank" rel="noopener noreferrer">https://trello.com/c[/O0M8W8X8](/archive/dev-news-briefs/2013-06-03/O0M8W8X8/</a>)</li> <li>Unicode fixes for displaying saved workflows in <strong>Tool Menu</strong>. <a href="https://trello.com/c/dAuDcE99" target="_blank" rel="noopener noreferrer">https://trello.com/c/dAuDcE99</a></li> <li>Unicode fixes for form builder and toolparameters. <a href="https://trello.com/c/nVldKDiL" target="_blank" rel="noopener noreferrer">https://trello.com/c/nVldKDiL</a></li> <li>Fix for <code>TabularToolDataTable.get_column_name_list()</code> when value column is overloaded by e.g. name. <a href="https://trello.com/c/6fPCLwn5" target="_blank" rel="noopener noreferrer">https://trello.com/c/6fPCLwn5</a></li> <li>Tool Parameter Validator: <code>MetadataInDataTableColumnValidator</code> fix issue where validator's list of valid options would become stale when e.g. a Data Manager was run. <a href="https://trello.com/c/dSEOinly" target="_blank" rel="noopener noreferrer">https://trello.com/c/dSEOinly</a></li> </ol> <br /> # Admin <ol> <li>Stop jobs on history deletion. <a href="https://trello.com/c/LBZxfcjx" target="_blank" rel="noopener noreferrer">https://trello.com/c/LBZxfcjx</a></li> <li>Track down decorator import failure that shows on some machines (see ticket). <a href="https://trello.com/c%5B/It6q5Ul8%5D(/archive/dev-news-briefs/2013-06-03/It6q5Ul8/" target="_blank" rel="noopener noreferrer">https://trello.com/c[/It6q5Ul8](/archive/dev-news-briefs/2013-06-03/It6q5Ul8/</a>)</li> <li>Do not allow deleted datasets to be viewed / downloaded. <a href="https://trello.com/c/elIs7IHc" target="_blank" rel="noopener noreferrer">https://trello.com/c/elIs7IHc</a></li> <li>Reports app: Fix util clash due to bad imports. <a href="https://trello.com/c/5d7EeeTq" target="_blank" rel="noopener noreferrer">https://trello.com/c/5d7EeeTq</a></li> </ol> <br /> # Core <ol> <li>Unify Web/API Transactions. <a href="https://trello.com/c/c5wZPVGd" target="_blank" rel="noopener noreferrer">https://trello.com/c/c5wZPVGd</a></li> <li>Eliminate <code>PasteScript</code> startup. <a href="https://trello.com/c/Q4bJNZuo" target="_blank" rel="noopener noreferrer">https://trello.com/c/Q4bJNZuo</a></li> <li>Upgraded <code>SQLAlchemy</code>. <a href="https://trello.com/c%5B/Q6kBeBy%5D(/archive/dev-news-briefs/2013-06-03/Q6kBeBy/)D" target="_blank" rel="noopener noreferrer">https://trello.com/c[/Q6kBeBy](/archive/dev-news-briefs/2013-06-03/Q6kBeBy/)D</a></li> <li>Error Logging with <code>Sentry</code>. <a href="https://trello.com/c/Yc1LXXTR" target="_blank" rel="noopener noreferrer">https://trello.com/c/Yc1LXXTR</a></li> </ol> <p><a href='/archive/dev-news-briefs/2013-06-03/'><div class="img-sizer" style="width: 600px"><img src="/images/news-graphics/2013_06_03_sentry-1.png" alt="sentry-1"></div></a></p> <p><a href='/archive/dev-news-briefs/2013-06-03/'><div class="img-sizer" style="width: 500px"><img src="/images/news-graphics/2013_06_03_sentry-2.png" alt="sentry-2"></div></a></p> <br /> # Pull Requests Merged <ol> <li>Significantly enhance job resource definitions. <a href="https://trello.com/c/uNpYoYov" target="_blank" rel="noopener noreferrer">https://trello.com/c/uNpYoYov</a></li> <li>More even distribution of job scheduling. <a href="https://trello.com/c/wBDXGcx2" target="_blank" rel="noopener noreferrer">https://trello.com/c/wBDXGcx2</a></li> <li>Workflows batch mode enhancements. <strong><a href="https://bitbucket.org/galaxy/galaxy-central/pull-request/75" target="_blank" rel="noopener noreferrer">#75</a></strong>. Thanks to <a href="http://jmchilton.net/" target="_blank" rel="noopener noreferrer">John Chilton</a>. <a href="https://trello.com/c%5B/UoBadE0f%5D(/archive/dev-news-briefs/2013-06-03/UoBadE0f/" target="_blank" rel="noopener noreferrer">https://trello.com/c[/UoBadE0f](/archive/dev-news-briefs/2013-06-03/UoBadE0f/</a>)</li> <li>Parallelism does work with from_work_dir attribute. <strong><a href="https://bitbucket.org/galaxy/galaxy-central/pull-request/156" target="_blank" rel="noopener noreferrer">#156</a></strong>. Thanks to <a href="http://jmchilton.net/" target="_blank" rel="noopener noreferrer">John Chilton</a>. <a href="https://trello.com/c/5fFZSCWn" target="_blank" rel="noopener noreferrer">https://trello.com/c/5fFZSCWn</a></li> <li>Galaxy Search Engine. <strong><a href="https://bitbucket.org/galaxy/galaxy-central/pull-request/137" target="_blank" rel="noopener noreferrer">#137</a></strong>. Thanks to <a href="https://bitbucket.org/kellrott" target="_blank" rel="noopener noreferrer">Kyle Ellrott</a>. <a href="https://trello.com/c/moZezGDP" target="_blank" rel="noopener noreferrer">https://trello.com/c/moZezGDP</a></li> <li>Validation on optional multi-select lists. <strong><a href="https://bitbucket.org/galaxy/galaxy-central/pull-request/154" target="_blank" rel="noopener noreferrer">#154</a></strong>. Thanks to <a href="http://jmchilton.net/" target="_blank" rel="noopener noreferrer">John Chilton</a>. <a href="https://trello.com/c/5PxgbL0b" target="_blank" rel="noopener noreferrer">https://trello.com/c/5PxgbL0b</a></li> </ol> <br /> # Security Fixes <p>Although there are no specific known security fixes in this distribution, all Galaxy instance maintainers are <em>strongly encouraged</em> to run the latest release to take advantage of other improvements and fixes.</p> <br /> # Bug Fixes <ol> <li>Dataset display now honors preview flag. <a href="https://trello.com/c/p7zeJHlX" target="_blank" rel="noopener noreferrer">https://trello.com/c/p7zeJHlX</a></li> <li>Bug fix to report's web application. <a href="https://trello.com/c/o0S3klAF" target="_blank" rel="noopener noreferrer">https://trello.com/c/o0S3klAF</a></li> <li>Correct display and masthead bugs upon logout/login cycle. <a href="https://trello.com/c/Dw0bUCv3" target="_blank" rel="noopener noreferrer">https://trello.com/c/Dw0bUCv3</a>, <a href="https://trello.com/c/cvzBIb63" target="_blank" rel="noopener noreferrer">https://trello.com/c/cvzBIb63</a></li> <li>Fix problem where jobs were unable to run when job limits were set. <a href="https://trello.com/c/6vxkqdjT" target="_blank" rel="noopener noreferrer">https://trello.com/c/6vxkqdjT</a></li> <li>Fix Bug causing both upload_async_message and tool_executed.mako to refresh the history panel on upload. <a href="https://trello.com/c/8urL3hGW" target="_blank" rel="noopener noreferrer">https://trello.com/c/8urL3hGW</a></li> <li>Fix Tophat2 Wrapper to properly quote read group attribute values. <a href="https://trello.com/c/nDBz5eoR" target="_blank" rel="noopener noreferrer">https://trello.com/c/nDBz5eoR</a></li> <li>Fix bug admin jobs <code>'AttributeError: 'NoopQueue'</code> object has no attribute 'job_lock'. <a href="https://trello.com/c/uBlCbOFs" target="_blank" rel="noopener noreferrer">https://trello.com/c/uBlCbOFs</a></li> <li><code>ToolDataTables</code>: Fix loading .loc files from locations other than galaxy's <code>tool_data</code>. <a href="https://trello.com/c/Xedp7bo5" target="_blank" rel="noopener noreferrer">https://trello.com/c/Xedp7bo5</a></li> <li>Fix API External Authentication. <a href="https://trello.com/c%5B/UjBbWw4%5D(/archive/dev-news-briefs/2013-06-03/UjBbWw4/)A" target="_blank" rel="noopener noreferrer">https://trello.com/c[/UjBbWw4](/archive/dev-news-briefs/2013-06-03/UjBbWw4/)A</a></li> <li>Fix non-persistent workflow step hiding. <a href="https://trello.com/c/sVKvrw67" target="_blank" rel="noopener noreferrer">https://trello.com/c/sVKvrw67</a></li> <li>Fix problem with search in workflow editor. <a href="https://trello.com/c/sAsC6lAK" target="_blank" rel="noopener noreferrer">https://trello.com/c/sAsC6lAK</a></li> <li>Fix to add confirm on delete permanently (footer button), saved histories. <a href="https://trello.com/c/8nUlUMew" target="_blank" rel="noopener noreferrer">https://trello.com/c/8nUlUMew</a></li> <li>"Stop job" function in jobs admin interface corrected (as of April 2013 release). <a href="https://trello.com/c/3vkBCaWf" target="_blank" rel="noopener noreferrer">https://trello.com/c/3vkBCaWf</a></li> </ol> <br /> # Project Updates <p><strong><a href="/news/">News</a></strong>, <strong><em><a href="http://wiki.galaxyproject.org/GalaxyUpdates/2013-06" target="_blank" rel="noopener noreferrer">June 2013 Galaxy Update</a></em></strong></p> <br /> <br /> # GCC2013 <div class='left'><a href='/events/gcc2013/'><img src="/images/logos/GCC2013Logo200.png" alt="2013 Galaxy Community Conference (GCC2013)" width="150" /></a></div> <br /> <br /> <br /> <br /> <br /> <br /> ---- <br /> # About <p><strong><a href="http://galaxyproject.org" target="_blank" rel="noopener noreferrer">GalaxyProject.org</a></strong></p> <p>The <strong><a href="http://wiki.galaxyproject.org/GalaxyTeam" target="_blank" rel="noopener noreferrer">Galaxy Team</a></strong> is a part of <strong><a href="http://www.bx.psu.edu/" target="_blank" rel="noopener noreferrer">BX</a></strong> at <a href="http://www.psu.edu/" target="_blank" rel="noopener noreferrer">Penn State</a>, and the <strong><a href="http://www.biology.emory.edu/" target="_blank" rel="noopener noreferrer">Biology</a></strong> and <strong><a href="http://www.mathcs.emory.edu/" target="_blank" rel="noopener noreferrer">Mathematics and Computer Science</a></strong> departments at <a href="http://www.emory.edu/home/index.html/" target="_blank" rel="noopener noreferrer">Emory University</a>.</p> <p><strong><a href="http://usegalaxy.org" target="_blank" rel="noopener noreferrer">Galaxy</a></strong> is supported in part by <a href="http://www.nsf.gov/" target="_blank" rel="noopener noreferrer">NSF</a>, <a href="http://www.genome.gov/" target="_blank" rel="noopener noreferrer">NHGRI</a>, the <a href="http://www.huck.psu.edu/" target="_blank" rel="noopener noreferrer">Huck Institutes of the Life Sciences</a>, and <a href="http://www.ics.psu.edu/" target="_blank" rel="noopener noreferrer">The Institute for CyberScience at Penn State</a>, and <a href="http://www.emory.edu/home/index.html" target="_blank" rel="noopener noreferrer">Emory University</a>.</p> <p>Join us at <strong>Twitter <a href="http://twitter.com/#galaxyproject" target="_blank" rel="noopener noreferrer">@galaxyproject</a></strong> or just read our tweets <strong>[Galaxy on Twitter](<a href="http://wiki.galaxyproject.org/Galaxy" target="_blank" rel="noopener noreferrer">http://wiki.galaxyproject.org/Galaxy</a> on Twitter)</strong></p> <p>Have a suggestion? Please see <strong><a href="http://wiki.galaxyproject.org/Issues" target="_blank" rel="noopener noreferrer">Using the Galaxy Issue Board</a></strong>.</p> </section> <div class="clearfix"></div> </div><footer data-v-54ece1d6 data-v-7b2abc5f></footer></main><footer class="static-footer" data-v-522248d2><div class="markdown container" data-v-522248d2><p><strong>usegalaxy.org</strong> is supported by NIH and NSF Grants HG006620, 1661497, and 1929694. 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