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Help on using Galaxy that is specific to particular browsers, operating systems, and/or hardware. This includes specific tricks and workarounds, as well as known issues.

Browsers

Firefox

Get Data from UCSC and Firefox >= 4 interaction

A bug in Firefox can cause data retrieval from the UCSC Table Browser to quietly fail.

Due to a regression introduced in a version of Firefox >= 4, if the browser is configured to reject third-party cookies, data retrieval from UCSC will quietly fail.  The steps to reproduce and symptoms are listed below:

  1. Select a Get DataUCSC ... tool in Galaxy.

  2. When finished in the Table Browser, click Send query to Galaxy

  3. The usual green message is displayed in Galaxy with the usual The following job has been successfully added to the queue: 1: UCSC ... message

  4. No new dataset appears in the history, even after refreshing

Upon clicking Send query ... at UCSC, your web browser generates a POST request containing the Table Browser's form contents and sends it directly to Galaxy as a tool/job submission, so there is no interaction between UCSC and Galaxy at this stage.  However, Firefox mistakenly believes that this is third-party site interaction and does not send Galaxy's session cookie along with the request.  The UCSC Get Data job runs, but the data is created in a new history in a new session which is not accessible to the current Galaxy user.

In its default configuration, Firefox is set to accept third-party cookies, so users should not encounter this issue unless their settings have been changed from the default.  In addition, the bug has already been fixed in development, but is targeted for release in Firefox 7.0 or 8.0.  Until the fix is released, the bug can be worked around in one of two ways:

Accept third-party cookies:

  1. From the Firefox (Mac) or Edit (others) menu, select Preferences

  2. Choose the Privacy section

  3. From the drop-down menu under History, choose Firefox will: Use custom settings for history

  4. Check Accept third-party cookies

  5. Close the Preferences dialog

Alternatively, you may grant Galaxy a cookie exception:

  1. Follow steps 1-3 above.

  2. Click the Exceptions... button found to the right of Accept cookies from sites

  3. Enter the hostname of the Galaxy server in the Address of web site: field (for the public Galaxy site at usegalaxy.org/main.g2.bx.psu.edu, use main.g2.bx.psu.edu)

  4. Click Allow to add it to the list.

  5. Click Close on this dialog and the Preferences dialog to return to the browser.