geWorkbench

Installation - top issues

Windows platform (maybe also Linux)

The Windows installers will not run if a version of Java higher than Java 8 update 51 is installed on the machine. For workarounds, see IMPORTANT Note for Windows (and_Linux).

Macintosh OSX platform

Gatekeeper stops files from running

The first time a downloaded file (e.g. a command file) is run, you may need to tell Gatekeeper to allow it to run. Please see instructions at IMPORTANT note for MacOSX.

geWorkbench 2.6.0

In the CNKB component, interactome export is currently only enabled for three smaller interactomes: BCi, HGi_Sun, and Geneways. Export of larger interactomes is being implemented through server-side changes and will be enabled in a subsequent update. However, export of larger interactomes directly into the Workspace is not recommended.

geWorkbench 2.6.0 and prior

Housekeeping Genes Normalizer and tab-delimited expression files

If a gene expression set is loaded into geWorkbench in tab-delimited format, the Housekeeping Genes Normalizer will not work. The workaround is to the save the data back to disk in the ".exp" format - to do this, right-click on the data node and select "Save". Then load the data back in to geWorkbench as format type ".exp". The Housekeeping Genes Normalizer can now be used.

MarkUs

Viewing MarkUs results directly in geWorkbench is only available when a 32-bit version of Java is being used. In all other cases, the MarkUs results can instead be opened in an external web browser. However, several steps, detailed in the MarkUs tutorial, are necessary to set up the use of Java in the web browser.

Cytoscape

When a gene network node is selected (left-click) within Cytoscape, and then right-clicked on, a detailed menu of annotation choices should appear. However, if the node is in the right quarter of the display box, the gene menu instantly disappears and is replaced by the background right-click menu. May occur in this and previous releases (Mantis issue #3194). To get the menu, decrease the network size (zoom out), or move the network left.

Sometimes, the first time Cytoscape is used in geWorkbench, the lower parameter window covers the entire component, so that the network diagram is hidden. It is hard to recognize this is what has happened, but the top of the panel can just be pulled down to reveal the network.

Use of incomplete annotation file causes errors in MRA-FET analysis

If an annotation file is loaded along with a microarray dataset, but the annotation file does not contain entries for all markers present in the dataset, then at least for the MRA-FET analysis, an incorrect result will be obtained. Mantis issue #3839.

PCA and 64-bit Java

The PCA 3D visualization does not currently work when using 64-bit Java, which is now the default on all platforms. It will work if a 32-bit version of Java is used to run geWorkbench (not available for Mac OS X).

PCA and OpenGL version

The PCA 3D viewer requires that the computer display driver support OpenGL version 1.2 or higher. If it does not, a warning message will be displayed at the time the user attempts to create a 3D plot. Any recent graphics card should provide this support.

BLAST

(first reported in 2.4.1) The NCBI BLAST server may occasionally return an error when sequences are searched from geWorkbench. The problem appears to depend on the load on the NCBI BLAST server. When multiple sequences are being submitted, geWorkbench submits them one-at-time to the BLAST server. When many sequences are submitted, it may be more likely that such a server-side problem will be encountered at some point and the search cancelled.

Running more than one copy of geWorkbench simultaneously

While running an analysis, some geWorkbench components write data to temporary files with non-unique names. For this reason, two copies of geWorkbench should not be running at the same time, and especially not running the same analysis.

Embedded browser not compatible with 64-bit Java

Affects: GSEA, MarkUs, Pudge.

Several geWorkbench components make use of a 32-bit embedded JDIC web browser. This browser will not display when using 64-bit Java JREs (now the default for geWorkbench on all platforms). If this situation is encountered, these components will instead offer a link to display the results in your computer's default web browser. However the displayed web page will not automatically update or interoperate with geWorkbench.

Astex viewer in MarkUs

Windows

The MarkUs results display includes the Astex molecular structure viewer, which is a Java applet. For this to run, a JRE must be available which matches the architecture (32 or 64-bit) of the browser being used. For Windows (as of early 2015), the default versions of Firefox and Chrome are 32-bit, so a 32-bit JRE must be installed on the computer to use this applet in the default browser versions.

As of February 2015, Chrome is available in a 64-bit version for Windows as a special download, and Firefox is planning a March release of a 64-bit version.

Getting Java

Particular versions of the Java JRE can be downloaded from http://java.oracle.com. 32-bit versions of the JRE include "x86" in their descriptions and "i586" in their file names. Additional information on configuring Java can be found on the MarkUs tutorial page.

Cytoscape loading

Cytoscape is by default enabled in the CCM. This is to prevent certain problems that have been seen if it is loaded later, after geWorkbench has completed its startup. If Cytoscape is unloaded and then later reloaded into the CCM, geWorkbench should be restarted. (c.f. Mantis issue #3381 and links to related issues therein).

Mac-related issues

Building from source on Apple Mac OS X (tested in Lion 10.7)

There is an issue with the Java 3D library included with Mac OS X. In order to build geWorkbench from source, one must either install certain files from J3D 1.5, or delete the PCA component from the geWorkbench components directory (#2495).

To configure J3D on the Mac, please see the instructions below.
To just remove the PCA component, find the geWorkbench installation directory and follow this path: components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule. In the gpmodule directory, delete the folder "pca".

Mouse-button issues (tested in OS X 10.7 Lion )

Right-click contextual menu: On the Mac, control-click can substitute for the PC's "right-click" action, and bring up a contextual menu. However, this is not implemented in geWorkbench on the Mac. The following work-arounds are available:
- Trackpad: In System Preferences, enable "Secondary click". You can choose 3 options on how this will work, including clicking in the lower-right-hand corner of the trackpad.
- Magic Mouse: In System Preferences, enable "Secondary click".

Cytoscape in 10.6.8

On OSX 10.6.8, but not 10.7 or later, an extra window may pop up when a network is displayed in Cytoscape. No workaround is known.

Grid Issues

For grid services hosted inside the Columbia firewall, the service metadata cannot be retrieved from outside the firewall. Instead, generic metadata will be displayed. You may see a delay of up to 30 seconds while geWorkbench attempts to retrieve the service metadata, before a timeout occurs and the generic metadata is substituted.

Previous Releases

For issues with previous releases, please see the Previous Release Issues page.

Configuring J3D on the Mac for gpmodule PCA

The Java3D version included in geworkbench is 1.5. On the Mac platform, an earlier version (1.3) is installed in /System/Library/Java/Extensions/. Unless this is fixed on the user's Mac,

geWorkbench cannot be built from source, as a compile error is generated, and
PCA 3D plots cannot be used on the Mac when the Installer version is used.

These problems arise because the j3d libraries in the system java extension directory have higher priority than those in geworkbench.

By copying the appropriate j3d and jogl files into a directory with higher precedence, these problems can be avoided. The following steps have been tested under Mac OS X 10.7 (Lion) but should work for other versions also.

The safest method is to place the updated files within the user's own directory structure. These changes will then apply only to that user and can be easily undone if needed.

If the directory ~/Library/Java/Extensions does not exist, create it, where "~" refers to the User's home directory.
- Note - in OS X 10.7 Lion, the ~/Library folder may be hidden by default. You can make it visible in the Finder by holding down the "option" key while selecting "Go" in the Finder menu.
- Alternatively, to make the ~/Library folder always visible, execute the following command in a terminal window:

 chflags nohidden ~/Library/
 You can undo this with
 chflags hidden ~/Library

Copy the following java3d 1.5 libs from the geworkbench installation to the java extensions directory ~/Library/Java/Extensions:
- geworkbench/lib/j3dcore.jar
- geworkbench/lib/j3dutils.jar
- geworkbench/lib/vecmath.jar

(Note - The java3d-1.5.1 files can also be downloaded from the Oracle Java3D distribution site).

Next, download the jogl libs, then extract and copy the following files from the extracted lib directory to the your own user extensions directory ~/Library/Java/Extensions:
- gluegen-rt.jar,
- jogl.jar,
- libgluegen-rt.jnilib,
- libjogl.jnilib,
- libjogl_awt.jnilib,
- libjogl_cg.jnilib

If you have system admin privileges on the machine, you can instead update the files for all users in /Library/Java/Extensions, however we do not recommend this.

General

Filtering a data set may after an analysis has already been run may invalidate objects that arose from the original, unfiltered dataset. Any filtering should be done before any analysis which creates child result nodes, e.g. a t-test, ANOVA etc.

Promoter panel (issue #1988) - under very particular conditions, where a letter has a score and height of zero, and where an external display is being used on a Macintosh computer, a graphics error can be reported to the console. However, this error does not cause any problems.