Former User of DNAx Community_41

Thanks! Similar to my question above, with respect to notebooks, is there a way for the upload to replace the previous version of file of the same name, instead of building up numerous copies?

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• 20 January 2023 15:44
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Thanks for all this helpful info! This is something I definitely will try in the future. For now, my functions are still in flux, which is why I was hoping for a way to keep them easily editable wh...

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• 20 January 2023 15:43
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Hmm, when I've accessed notebooks from the DNAnexus tab, I've found this to be the case. But when I download and upload, I find that I just end up with a new copy of the file, and it leaves the old...

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• 20 January 2023 15:42
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Importing functions from one Jupyter notebook (or Python script) to another within a DNAnexus JupyterLab session

Hi! I have a number of Python functions that I've written and wish to import into multiple Jupyter notebooks to avoid copy-and-pasting those function definitions repeatedly. Normally, I would just ...

• Former User of DNAx Community_41
• 19 January 2023 00:00
• 3 followers
• 9 comments
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Perfect, thanks so much!

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• 21 November 2022 15:18
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Downloading or searching job logs -- where are they?

Hi! I am trying to search through all the job logs for jobs with a specific tag to see which ones threw a specific warning in stderr. Is there a way to do this more efficiently than navigating to e...

• Former User of DNAx Community_41
• 17 November 2022 00:00
• 2 followers
• 2 comments
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Trouble using $in_prefix and $in_name with swiss-army-knife

Hi! I'm hoping to set up a batch job to extract filters from the vcf files stored atBulk/Exome sequences_Alternative exome processing/Exome variant call files (gnomAD) (VCFs)/. I've been testing ou...

• Former User of DNAx Community_41
• 09 November 2022 00:00
• 1 follower
• 2 comments
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gzip can't be run in aws:eu-west2?

Hi, I was wondering if anyone has found a way to compress generated files on the Research Analysis Platform using gzip. When I try to run "dx run gzip," I get the error: dxpy.exceptions.InvalidStat...

• Former User of DNAx Community_41
• 28 October 2022 00:00
• 1 follower
• 1 comment
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Thank you, this is extremely helpful! I ended up specifying the full file path to the notebook within the run command (eg -iin="project-####:/path/to/input_notebook.ipynb") and then only the file n...

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• 14 October 2022 13:20
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