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ballaxyPlugin
Recent versions (starting from the development snapshot V1.4.79) of BALLView (http://www.ballview.org) come with a plugin that simplifies interacting with a ballaxy instance. To activate the plugin, open BALLView's preferences and navigate to the "Plugins" - submenu. The list on the right hand side should show an entry with the name "BALLaxy". If this entry does not appear, make sure that you installed a BALLView version with ballaxy - support (if you compiled BALLView from source, make sure that it has been compiled with QT_WEBKIT - support enabled). If the plugin has been installed into a non-standard location, you can try adding the corresponding directory to the list of plugin directories by pressing the green "add" button. Make sure that the plugin has been activated, i.e., that it appears as "BALLaxy (active)". Otherwise, highlight the plugin and press the "activate" - button.
Once the plugin has been activated, you can set its preferences by clicking on the small arrow next to the "Plugins" - entry in the prefences dialog. Click on the "BALLAXYPlugin" - entry to change the ballaxy url (defaulting to http://ballaxy.bioinf.uni-sb.de), if desired. You can also provide login details in this dialog, but please note that the login data will be stored in plaintext in BALLView's .ini file.
After closing the preferences, you might already see a window with the title "BALLaxy". If not, click on the "Windows" - menu and activate the "BALLaxy" - entry. Please note that the default position of the window might not leave sufficient room to properly display the page. In this case, grab the title bar and move the window to its desired location and resize it sufficiently.
You will now be able to use the ballaxy service from the window displayed in BALLView. Structures can be easily exchanged between BALLView and BALLaxy. To test this mechanism, load or create a structure in BALLView (e.g., by using Build=>Build Peptide). Then, right click on the molecule in the "Structures" window and select "Upload to ballaxy" from the context menu. After a few seconds, the upload should start and the molecule should automatically appear in your ballaxy history. Now, you can run arbitrary workflows or tools on the molecule (e.g., the BondOrderAssigner). To download the results back to BALLView, click on a molecular entry in the ballaxy history to open it, then click on the save-button. The molecule should be automatically downloaded and added into BALLView's structure window.