ENA submission receipt: Excel input formatting and troubleshooting

[jennaj]

Hi @janslet

I’d like to get this solved for you!

How to create a testing history for method development and troubleshooting!

Let’s start over in a new history in the sharable storage space for the troubleshooting. Then, you can move back into other storage choices for the real runs. You’ll have 2 TB of space at the UseGalaxy.eu servers which should be plenty for this type of exploratory work.

You will be able to develop a reusable workflow that can be run in any history or any data storage space, and possibly any Galaxy server! If this is new to you, this is a nice Introduction to Workflows.

Steps

1. Create a new history, give it a unique name, and set the History Preferred Storage location to the Short term storage

   Click on the storage icon to reach the directions

   

   Click on that Preferred Storage pop-up window, to reach the per-History Preferred Storage choices, and choose Short term storage. This will only impact this history where we will be troubleshooting your job.

   

2. Upload some of your samples

   Do this as an upload step, not from a copy from another history. You don’t need to add all of your full data, just enough to represent the different types of input data.

   For your use case, this would be including a representative example of R1+R2 pairs, and the “R-nfilt” and “nfilt” types. Or, you can go ahead and load all samples and we can help to subset later on as we do the testing and development work.

3. Upload your metadata file in xlsx format

   Also do this one as an Upload step, not a copy from another history. Don’t worry about filtering it down to match your sub-samples (if you choose to do that). Just load the original file.

   Load one copy using all default settings with the Upload tool.

   Then, please also load another copy of the same file, into the same history, and select the datatype xlsx in the Upload tool. We will use this as a comparison.

4. Upload your metadata file in tsv or csv format

   In Excel on your own computer, export a tsv (tab separated) or csv (comma separated) version of your metadata file. Please do not adjust the file name or extensions. We want the data exactly as it is created by Excel.

   Then, Upload this exported file to your Galaxy history, using all default settings.

   Once in Galaxy, please do not make any adjustments, we want the plain text file in the original format as a baseline dataset as another comparison.

   If you want to export and then load both a tsv and csv version, that would be great! More data and more details is always better.

5. Finally, try to run the target tool!

   It is okay if this fails. We will want to inspect how you are selecting the input datasets and the exact parameter settings, plus the tool version choice and the job logs. Your run will capture all of these details.

   If you need to organize the dataset samples into a collection, go ahead and do that to prepare the data for input to the tool. Make sure to do this step in the same testing history, and as a new manipulation. We don’t want any data or manipulations copied from any other history.

   If you want to try the run a few different ways, that would be great! With collections, without, possibly different parameter settings. Just be sure to do all of this work in our testing history.

6. Once done, and if the tool still fails, please generate a history share link and post that back here for review. Toggle just the first sharing option Make History accessible. Leave the other options at default or we won’t be able to review, or test out changes, or help you to build up a workflow for reuse against your full final data run in permanent storage.

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Hope this helps and I’ll watch for your replies!