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GenePattern 3.8.0 debuted an updated user interface, and a number of new features, such
as the support for pinning modules, the ability to place a pipeline in multiple categories,
the creation of dynamically populated drop downs in modules, and file purge settings
based on user or group id, to name a few. We will review these and other features in
this video overview of GenePattern 3.8.0. In GenePattern 3.8.0 we have, perhaps most
obviously, redesigned the Modules & Pipelines panel, and combined it with the Recent Jobs/Uploads
panel, so that all tabs for Modules, Jobs and Files (to include any GenomeSpace associations)
now appear only on the left hand of the GenePattern server page.
You will notice that the full list of modules is no longer shown along the left side of
the screen. In order to browse modules & pipelines, simply
click the Browse Modules button. This then displays a sliding panel where you may choose
to browse modules by category, by suite, or display the full list of modules. In each
case the ordering is alphabetical. Searching for modules in GenePattern 3.8.0
is much the same as it was in 3.7.0. Typing in the search box will begin to filter for
modules and pipelines that match what you have entered. However, in 3.8.0, this is no
longer limited to simply the module name. We now search over the module name, description
and any suites or categories that are associated with the modules and pipelines. Thus allowing
you to more easily find a module, even if you are unsure of its name, but do know what
function you seek. A new feature in 3.8.0 is the ability to pin
a module or pipeline to the left hand panel. To accomplish this you simply search or browse
for a module or pipeline and then drag the desired object into the “Favorite Modules”
area on the left. the gear icons displayed in the upper right
of the module or pipeline provides a link to the documenation.
As previously mentioned, one of the more obvious updates to 3.8.0 is the consolidation of the
Modules & Pipelines panel with the Recent Jobs, Uploads and GenomeSpace panel. These
are all now located on the left, but continue to display the same information as before,
when the tab is selected. Note also that recently used modules are still
displayed at the bottom of the Modules & Pipelines panel when the Modules tab is selected.
Moving on to the Run Task form, we find an improvement in our support for running batch
jobs. After checking the “Batch” box in the upper right corner of the desired parameter,
you can drag in files or directories to create your list of files for the batch job.
As mentioned at the beginning of this video, we’ve added the ability to give multiple
categories to a pipeline, thus allowing it to appear in places other than under just
the “pipeline” category. For instance a pipeline could be given a functional category,
such as “RNA-seq” in addition to, or instead of, the pipeline category.
For those users with module creation privileges, you may be happy to know that we now support
the creation of dynamic drop-down lists, where the elements in the list refer to directories,
rather than only to files. When selected, the entire contents of the directory will
be uploaded to the GenePattern server. This benefits modules whose dropdowns required
multiple files to be retrieved, such as BWA or TopHat. For those of you using these modules,
it means you will have more timely access to data you’ve requested be added to these
sorts of drop-down file lists, as the module developers only need add a file to a directory
to have it appear, rather than release a whole new version of a module or pipeline.
For those of you who are GenePattern administrators, we’ve now added the ability to set file
purge intervals on a per-user and per-group basis, thus overriding the system-wide purge
setting for those users and groups. Instructions for this can be found on the File Purge Settings
page, in the Administration section of the server ui. For those of you on our hosted
server, please contact us if you think this might be of use to you.
More information about these and other features, as well as bug fixes in GenePattern 3.8.0
can be found in our 3.8.0 Release Notes, available from the Help menu, if you are are on a GenePattern
server, or from our website, genepattern.org, under Documentation/Tutorials, in the menu
on the left. More information about GenePattern can be
found at genepattern.org. For notification of updates to our server,
modules & pipelines, and other GenePattern news, please follow us on Twitter, Facebook
or Google+, by searching for GenePattern, or by clicking on the links on our website.