link EBI data retrieval into the filter/plot/explore #4411
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Hi @wee-snufkin! Exciting! |
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@Camila-goclowski it will also eventually be good to link this to the Seurat version you're doing |
| # Conclusion | ||
| Now you can use this object as input for the [Filter, Plot, Explore tutorial]({% link topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.md %}) and its associated workflow! | ||
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| Even though this tutorial was designed specifically to modify the AnnData object to be compatible with the subsequent tutorial, it also shows useful tools that you can use for your own, independent data analysis. You can find the [workflow]() and the [answer key history](). However, if you want to use the workflow from this tutorial, you have to keep in mind that different datasets may have different column names. So you have to check them first, and only then you can modify them. |
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Here is something missing [workflow]() and the [answer key history]()
| @@ -108,6 +108,12 @@ You can access the data for this tutorial in multiple ways: | |||
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| {: .hands_on} | |||
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| 4. **Importing data from EBI Single Cell Expression Atlas** | |||
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| You can also pull the data from publicly available [Single Cell Expression Atlas](https://www.ebi.ac.uk/gxa/sc/home). You can simply access the dataset we are working on by using the tool *EBI SCXA Data Retrieval* with experiment id of [E-MTAB-6945](https://www.ebi.ac.uk/gxa/sc/experiments/E-MTAB-6945/downloads). This [short tutorial]() will show you how to use this tool and modify the output so that it's compatible with this tutorial and its workflow. | |||
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here as well [short tutorial]()
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Thanks @bgruening, I'll fill the links once EBI retrieval tool starts working again and allows me to generate the final history and workflow! |
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@wee-snufkin can I help to fix the tool? |
only one image so putting here
It's all sorted! :) |
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| > 1. {% tool [Scanpy Read10x](toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy9) %} | ||
| > 2. Make sure you are using version **1.8.1+galaxy9** of the tool (change by clicking on {% icon tool-versions %} Versions button): |
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@wee-snufkin what is broken in the latest version?
Should we hide this latest version?
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That's the error message when I'm running this step with 1.8.1+galaxy93
If it's not a quick fix, we might want to hide the latest version
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This error is fixable. We just need an older numpy version. e.g. numpy==1.21
Can you try this on EU please with the latest version? If this works I will fix the upstream package.
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@pcm32 This is a matter of tool developer skills, if I'm not mistaken? Are you able to advise here?
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We don't seem to get this error on instances using singularity (although not sure at the exact wrapper version). Those newer versions only have changes in the galaxy wrapper, the dependency had remained the same for a long time I think
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So what's going on with this? I'm reviewing this following @wee-snufkin instructions in the tutorial to use the older version. If this issue gets fixed, we can update it I guess
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I've copied this discussion over to here so we don't lose it in the merged PR: galaxyproject/tools-iuc#5636
Co-authored-by: Pavankumar Videm <[email protected]>
Edit overview section final fix Ignore the suggestion Added explanation/introduction at beginning update intro statement
update metadata explanations fix labelling in hints
To be expanded when we have more seurat tutorials
Adding another option for getting data into filter, plot, explore tutorial. Uses EBI data retrieval tool and some data manipulation to integrate well into the tutorial and its workflow.
@nomadscientist