Question about tool errors in an older Galaxy release

With an older Galaxy release, and older versions of tools, or some mix of updated Galaxy/not and updated tool versions/not … many things can go wrong.

The error indicates that the datatype assigned to the fastq data is a mismatch for the actual data format. This used to happen if the fastq data is labeled as being compressed when it is not, or the reverse. It can also occur if a dataset is truncated or has some type of internal formatting problem.

You could try to figure out what the actual format is and assign the correct datatype and try the tool again (rerun). Or fix what is wrong (truncated end of file?), reupload, run again, etc.

The best way forward, to avoid other problems, would be to update your Galaxy instance to the most current release and to also update your tools to the most current version.

Be aware that Solexa data is a much older format and is not really supported anymore – so do your updates with that in mind. Or don’t update and do your best to work around/solve some of the usage problems that might come up when working with older releases/tools.

The Galaxy FAQs address common troubleshooting solutions. These are based on the newer releases, but the basics apply to bioinformatics in general (in Galaxy or not).

In short: Tools are picky about inputs! Correct file/dataset format matters. Assigned datatype matters. More has been added to Galaxy to help people avoid usage issues but not everything odd can be captured, and the earlier releases/tool versions don’t have all of the latest upgrades/UI-assists. Unless you update, you’ll need to work through any problems encountered, and sorting out old bugs (now resolved) apart from actual new bugs (rare) from usage issues (common) will be a challenge, yet is certainly possible, and will still be easier than setting up the same experiment correctly line-command. Plus, working line-command you’ll lose the other parts of Galaxy’s reproducibility bonuses: histories, workflows, sharing.

Hope that helps!