On Thu, Dec 30, 2010 at 12:05 PM, Bossers, Alex <Alex.Bossers@wur.nl> wrote:
Peter,
I have tested the XML parser for blast jobs on a larger set of files. I haven't checked every detail yet but it seems to process it now without problems. Majority tested using blastp on two protein databases with over 2k queries.
Hi Alex, That's good news :)
Another point I already mailed you off list is the ability to capture additional STDOUT and/or STDERR in a log file. Warnings make the galaxy tool run red and you have to view->save->importnew.... which is cumbersome and waste of time and resources when files are over 1.5G big. These files processed without any problem though in the xml parser!
Sadly true, As I said off line, I found this too just before our Institute closed for Christmas, again harmless blastp warnings about Selenocysteine on stderr causing Galaxy to treat it as an failing job. Ideally this will be fixed in Galaxy: http://bitbucket.org/galaxy/galaxy-central/issue/325/allow-tool-authors-to-d... In the short term, I plan to try modifying the BLAST+ wrapper XML files to redirect stderr to stdout. That way Galaxy will show the warning in the jobs's info text. There will be lots of little tasks like this will be waiting for me back at work in the new year :(
Thanks and keep up the good work (many people don't realize all hassle you have to go through when wanting/making a tool available via tool_shed to others..
Your testing is also much appreciated, and is important as I expect every Galaxy installation will be slightly different. Regards, Peter