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Question: reproducibility - software version and parameters in the history
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gravatar for a_kathrin
23 months ago by
a_kathrin • 10
a_kathrin • 10 wrote:

Hello,

for the reproducibility of the analysis I would expect that the Galaxy history would include the software version and the parameters used for each step of the analysis, but it seems that this is not the case. At least you cannot read them in the "view details" content. Are they reported somewhere else?

Thank you all
galaxy • 524 views
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modified 23 months ago by Jennifer Hillman Jackson ♦ 25k • written 23 months ago by a_kathrin • 10
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gravatar for Jennifer Hillman Jackson
23 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Details per tool can be found on the "View details" display (the "i" info icon). Parameters and other details are reported. Tool versions, that are included in the source repository, will display. Be aware that some older tools version/wrappers do not report this always, yet most newer ones do. In particular, those from the authors devteam and iuc include tool versions, following these group's coding standards.

To review all datasets in batch with parameters, use the History menu (gear icon) option "Show structure". Please note that at http://usegalaxy.org right now (today), this function is problematic. Our team is working to correct it. The local 16.07 Galaxy I tested this on displays the information without issue.

For citations in batch, use the History menu option "Export tool citations". Only tools wrapped with this information will have it included through this function.

Workflows will also batch display all tool with parameters, using the "View" option on the Workflow page's drop-down menu per workflow.

Tool versions are not yet reported on the batch functions but are a planned (and important) functionality. Related ticket: https://github.com/galaxyproject/galaxy/issues/2882

Hopefully this helps, Jen, Galaxy team
ADD COMMENT • link written 23 months ago by Jennifer Hillman Jackson ♦ 25k
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