I'm trying to get DEXSeq to run in Galaxy. I'm able to get the older version 1.24 to run in Galaxy, however, due to DEXSeq - dexseq_count.py issue the generation of the HTML reports would fail. So, I updated the Bioconda package to the latest supported by Bioconda (1.26.0) and updated the DEXSeq Galaxy wrapper.
The tests for the Galaxy wrapper seem to run fine, however, when I try to run DEXSeq on real data, version 1.26.0 runs for more than a day without completing (and then gets killed by our scheduler). Running version 1.24.0 on the same data finishes in about three hours.
Are there any known issues in 1.26 that would cause this? Any ideas on troubleshooting this? Perhaps options to change? Thanks for any advice.