1- I am using Tuxedo for tomato. I run the workflow from the shared data.
In the TopHat section in Tuxedo there are the following sections:
Output dataset 'output' from step 1 Use a built in reference genome or own from your history Use a built-in genome Select a reference genome If your genome of interest is not listed, contact the Galaxy team TopHat settings to use
However, it is not possible to choose any option for built in reference genome or from your own history. This is written just in the text format and I am not able to choose any of them - I need "from your own history" option.
2- Alternatively, I tried to use TopHat - not form tuxedo - but form the tools section, but the job list stays grey - not yellow or green - and it seems it does not work at all.
Many thanks in advance,