So I still owe an explanation of how I got Biomart working. (Basically, recompiling a bunch of stuff with ARCHFLAGS=anything I could throw in. But there's a few other tips I should add.)
Meanwhile, I followed the directions in the Getting Started section of the PDF to create a data set with one table. It seems to be working! 1. If I now have a bunch of new data for the tables, how do I get it in there? Am I supposed to load the data into my "raw" schema (the one martBuilder plays with) and drop all the tables in my final schema and recreate them using the SQL martBuilder gives me? 2. In other bad news, martEditor isn't saving for me. If I try "Save All", it lets me browse to a location on disk, but then doesn't save a file there. (I even tried saving in /tmp/ in case there was some weird permission issue.) Also, if I Export All, nothing changes (even if I restart Apache, which I tried out of desperation). Actually, it's worse than that: it seems like it saved (that is, exported) some of the martEditor changes I made, but then a different time I changed things it didn't save. Can you tell me where it would be saving things and why it would sometimes work? And while the changes sometimes show up in martEditor, they're never visible in the actual web page. 3. Also, assuming I input new data into the mart (see #1), how do I get dropdowns to reflect the new set of possible values? If I select "insert dropdown" or whatever, it creates all of the filter values anew, which means I have two copies of some of the values. (Of course, I can't really tell what's going on since nothing changes in the web page.) 4. Is there an easy way to reorder options? If I have six options, how do I move option 4 to be in between option 2 and 3? Anywhere I try to drag, option 4 ends up being placed INSIDE either option 2 or 3. I only managed to reorder by dragging everything in my required order into the container object. 4a. In the end I may be happier editing the XML file, but I don't know where it is right now, and for some changes, it might be nice to use martEditor. Help! -Amir Karger
