# Cuff Suite Not Running -- Deprecated Tool Suite

**URL:** <https://help.galaxyproject.org/t/cuff-suite-not-running-deprecated-tool-suite/2298>\
**Category:** Uncategorized\
**Tags:** gtn-tutorial, deprecated, tool-deprecated\
**Created:** [October 17, 2019, 6:44pm UTC](https://help.galaxyproject.org/t/cuff-suite-not-running-deprecated-tool-suite/2298 "2019-10-17T18:44:03Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![rpotens007](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/rpotens007/32/1172_2.png) [@rpotens007](https://help.galaxyproject.org/u/rpotens007)\
**Post date:** [October 17, 2019, 6:44pm UTC](https://help.galaxyproject.org/t/cuff-suite-not-running-deprecated-tool-suite/2298/1 "2019-10-17T18:44:03Z")

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Cufflinks, Cuffcompare, and Cuffnorm stopped running. I tried resume paused jobs but still paused.

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [October 17, 2019, 10:09pm UTC](https://help.galaxyproject.org/t/cuff-suite-not-running-deprecated-tool-suite/2298/2 "2019-10-17T22:09:37Z")

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Hi @rpotens007

All of these tools are deprecated and should be avoided. They are no longer maintained and several include known bugs that will never be addressed.

Even if they work (do not fail or stall out), unexpected scientific results can occur that are not always obvious to detect.

Try the updated methods in the “Transcriptomics” GTN tutorials instead:

> [@Troubleshooting resources for errors or unexpected results](https://help.galaxyproject.org/t/troubleshooting-resources-for-errors-or-unexpected-results/42/1):
>
> [Galaxy Training Network Tutorials](https://training.galaxyproject.org): Some [GTN](https://galaxyproject.org/teach/gtn/) tutorials are appropriate for [Galaxy Main](https://usegalaxy.org) and some are not. Where you can run each is noted per tutorial – click on the _Galaxy instances_ gear icon ![galaxyserversGTN](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/1X/1287f50cfcdaa1aad750fe323f96995260ac4947.png) to review the [Public Galaxy](https://galaxyproject.org/use/) server choices. If a tutorial is supported by a pre-configured [Galaxy Docker](https://hub.docker.com/r/bgruening/galaxy-stable/) training image, instructions for how to get it will be listed below the tutorial listings, per category.

Troubleshooting tips that cover the updated tools/methods should you run into problems:

- [Extended Help for Differential Expression Analysis Tools](https://galaxyproject.org/support/diff-expression/)