On Thu, Jun 2, 2011 at 10:53 AM, Peter Cock p.j.a.cock@googlemail.com wrote:
Now that I have a local Blast2GO database, I'll be able to try out b2g4pipe on some bigger XML files (without having to wait ages).
It turns out that Blast2GO haven't fixed a Java heap space problem with their parser and large NCBI BLAST+ XML files yet - their suggested workaround as of Oct 2009 is to split them or reformat them to act like older versions of BLAST. I've updated the wrapper to do this, and tested it on a 700MB BLAST XML file. The update is now on the tool shed.
Further work (after discussion with Gerrit) to support the optional Blast2GO project file (*.dat) and an optional InterProScan XML input file will ideally need to have extra file formats defined in Galaxy, thus this thread:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-June/005620.html
Peter