My histories seem to be stopping their processing around the Tophat-cuffmerge steps since the change over of Galaxy online. Sometimes a red box appears over my history name but disappears in a minute or less.

I am wondering, given the way the Toolshed now looks different for RNAseq work,  if some changes have been made that are disallowing the procedures I used previously.

For example:

I run larger Fastq files (100 million to 200 million 50bp single-ended reads per sample).  I have been grooming my illumina fastq's, using Tophat (not Tophat2) for alignment, then Cuffmerge, then Cuffdiff.  This worked in the past but my history are just getting thru Tophat or Cuffmerge and stalling.  Should I be doing this in a different manner?

This has been my second time around with these datasets after it was suggested that I delete and start all over again.

Elwood Linney