Thank you very much for this detailed descriptions. You have discovered 2 bugs at once, here the explanation:
1. With the release of IntOGen Mutations, the URL for IntOGen has changed and thus the error message when you try to import data from IntOGen arrays (the old version).
2. We have already discovered that the Java upate 25 of Java 7 is letting components of Dialogs disappear (see https://github.com/gitools/gitools/issues/104
) and we think you may have the same problem. Could you please confirm on which Java version Gitools is running? We have prepared a webstart for Gitools that will thell you the exact version. Please follow the instructions below:
- Select the menu "Help -> About Gitools" and please report the version you will find in the pop-up window.
If you have Java 7u25, there are two existing solutions:
- If you like, you could try if the problem is solved with Java 7u40.
Some remarks about IntOGen data. The tutorial you were following would import data from the submodule of IntOGen which now is called IntOGen arrays. If you would like to browse mutation data or other cancer genomics data from TCGA and TCGA Pancancer I'd propose that you go to www.gitools.org/datasets
, they are best fit to show the new capabilities that Gitools 2.0.0 will have.
Thanks for your time,