I would like to know the changes and updates that trinity and its dependencies has undergone since 2019, since in November of that year I performed a transcriptome assembly, which I have recently repeated with Trinity from command line and the assembly statistics I have obtained are very different from the one I performed in 2019. Could anyone help me, I would like to replicate this run, and even if I don’t get the same results as that time, they should be similar to be sure that I am running it on command line just like I did in 2019 in usegalaxy.
Thanks for your help in advanced.
The version of
Trinity as wrapped for Galaxy is included on the “Job Details” page (“i” icon within a dataset) associated with the output dataset. Parameters, dependencies, and the command-line executed are also included.
To review the history of development changes to a tool wrapper (any), including the tool wrapper details and other dependencies like the version of command line tools included in the runtime environment, please see the Tool Shed https://toolshed.g2.bx.psu.edu/.
If you still have the original run in Galaxy, then you can use the “rerun” icon to bring up the original tool form.
You could adjust the tool version at this point (to the most current) and rerun if you wanted to. This might give you more information about what is going on. Is the result the same when rerun in Galaxy? But the original and/or rerun is not the same as the command line? There is probably a parameter difference.
Or, to just review the original tool details (technical changes), in the upper right corner is an “Options” menu – click into the “View in Tool Shed” choice. Screenshot of that menu
If you don’t have the original run still in Galaxy, search the Tool Shed with the tool name and navigate through the versions until it matches what you used before.
The development repository and any external sites (original author dev/help) are all linked from that Tool Shed view.
Hope that helps!