geWorkbench

Installation - top issues

Macintosh OSX platform

Gatekeeper stops files from running

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

geWorkbench 2.6.0 and prior

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.

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

The PCA 3D Viewer does not work on the Mac OS X with Java 7 (64bit).

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.

Any current release

Java plug-in in web browsers

In some cases, geWorkbench uses an external browser window for results display, and may also use a Java applet in that window for results display.

Because of this, you may need to specifically enable Java Plugins to run in your particular browser. You should be prompted by the browser to allow this. After you are finished with the tool, you may wish to disable Java applets in your browser again. These controls are usually found in the browser's settings menu.

In addition, there are platform-specific steps that may need to be taken, as detailed below.

Some Java applet-based tools (such as MarkUs) require that the 32-bit version of Java be installed. Even if you have a 64-bit version of Java installed, you should also install the 32-bit version to use these components.

Windows

Some geWorkbench components, such as MarkUs, use a Java-based applet that runs in your web browser. If the applet does not run, you can allow it by taking the following steps: 1. In the Windows Control Panel, click on the Java icon to start the Java Control Panel.

2. In the Java Control Panel, click on the Security tab.

3. Check-mark the box "Enable Java content in the browser".

4. Push the "Edit Site List" button.

5. Add an exception to the Exception Site list in the lower part of the dialog for the page containing the Java applet.

5a. For MarkUs, add "https://honiglab.c2b2.columbia.edu" (without the quotes).

The above has been tested to work on Windows 8.1 with Java 7 update 51.

64-bit Java issue

Affects: GSEA, Markus, Pudge and PCA.

Several geWorkbench components make use of the embedded JDIC web browser. The version of JDIC used in geWorkbench is not entirely compatible with 64-bit versions of Java. If this problem is encountered, these components will instead transfer the display to your computer's default web browser. However the displayed web page will not automatically update or interoperate with geWorkbench.

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.