A search box on the home page allows users to find modules by typing names or parts of names. The results are presented in a
dynamic Google search style.
Users can now view all files they have uploaded and use them in any future analysis via the Uploads tab on the home page.
Job Output Subfolders
Users can now browse files in subfolders on the Job Status page, enabling users to directly use those files as module input.
In addition, users can download jobs with the subdirectories preserved.
The 3.3 release fixes issues in several functional areas of GenePattern, including:
GenePattern server configuration
GenePattern 3.3 extensively refactors the GenePattern pipeline engine to fix the following issues:
pipelines handle optional input parameters without errors
output files from nested pipelines are passed to the outer pipeline
pipelines are checked for missing modules before they run, eliminating this as a source of errors
pipelines run asynchronously, allowing pipeline jobs to resume after a server restart
running pipelines can be terminated without leaving child jobs in invalid states, reducing resource use
pipeline status is shown correctly on the Job Status page for terminated or failed pipeline runs
failed jobs within pipelines are shown as errors
execution of pipelines is streamlined to reduce resource consumption
GenePattern 3.3 provides improvements to job execution and configuration:
job configuration file errors are displayed on the server settings job configuration page
job analysis is prevented from using all the available database connections
GenePattern 3.3 improves the integration between GenePattern and the LSF batch queuing system:
jobs are not permanently stuck in invalid states if the GenePattern server encounters problems submitting jobs to LSF
the error messages are more informative when errors occur with LSF job submissions
LSF jobs can be terminated immediately, rather than being queued for termination
a pending LSF job can be terminated
GenePattern server configuration is improved in this release, allowing server administrators to:
reload the job configuration file programmatically without a server restart
configure properties based on users and groups
suspend or start the job queue from the job configuration page
customize the location of the jobs directory
customize the location of each user's uploads directory
prevent new jobs from being added if disk space is almost full
GenePattern 3.3 includes a number of other bug fixes and improvements:
the GenePattern web front end can better handle running under a heavy load, providing shorter load times for the Pipeline Designer and
Job Results pages
modules do not fail when the GenePattern server is installed in the default location on a 64-bit Windows machine
(C:Program Files (x86)GenePatternServer) (Note: See Known Issues for the exception.)
the GenePattern server retains custom server variable values on restart
the Pipeline Designer page sorts modules versions numerically, rather than alphabetically
more than one job can be deleted from the Job Summary page at a time
request parameters are preserved even if there is a login dialog as an intermediate step
modules retain input file specifications on reload even if the parameter names are similar
pop-up menu contents for the job results files present correct options
the GenePattern installer can handle port specifications
These features are in development. While they are present in the GenePattern 3.3 code, they are turned off by default. If you would like
to help us test them, please contact us at firstname.lastname@example.org for instructions for turning these
features on in your GenePattern server installation.
Advanced Upload for Large Input Files
This feature implements a new file upload system for handling input files larger than 2 GB. This is available in individual modules
(select the Advanced Upload radio button) and the Uploads tab, and enables batch execution and the directory input parameter, as described below.
Users can select multiple files in a folder via the Advanced Upload feature. The module will be run once for each file selected.
New Input Parameter: directory
Module developers can specify an input parameter as a directory. The user can then select a directory of input files for the module,
rather than a single input file. All the files in this directory are treated as input for a single run of the module. Using this
parameter type invokes the Advanced Upload option.
Upload Files via the Uploads Tab
Users can upload files without running a module by using the Upload Files button in the Uploads tab. Uploaded files can used in any future analysis.
Important Note: When users run a job normally, the job input files are scheduled to be purged 7 days after the job run (on the Broad public
server and on servers where the default time is in place). However, when users upload a file directly, the files are not scheduled for deletion at
all. Uploaded files must be manually deleted from the server.
Known issues in GenePattern 3.3 include:
ComparativeMarkerSelection will fail when run on a GenePattern server installed in the default location of a 64-bit Windows machine.
Other Java modules that invoke R with the command line " -DR= ..." are likely to fail as well. Workaround: Edit the R 2.5 Home
setting on the Programming Languages page to change to the default GenePattern install location (C:Program Files (x86)GenePatternServer).
GenePattern does not support module names with spaces in them.
Some GenePattern modules do not work when the input filename contains a space character. Workaround: Rename the input file without a space
On Macintosh: Java Runtime Environment (JRE) 1.6.0_15 does not work. Workaround: The GenePattern team suggests updating to the most recent
JRE (GenePattern 3.3 has been tested with 1.6.0_20 and above)
On Windows 7/Vista: The StartGenePatternServer and StopGenePatternServer applications must be run as an administrator. To start or stop
the GenePattern server, right-click on StartGenePatternServer.exe or StopGenePattnerServer.exe and select Run as administrator.
For GenePattern administrators who have changed the "input.file.mode" property (in the genepattern.properties file) from default:
GenePattern 3.3 only works with the default setting, input.file.mode=path.