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  • Jan 07 2019 15:05
    colindaven starred ewels/MegaQC
  • Dec 10 2018 16:46
    vzg100 starred ewels/MegaQC
  • Dec 10 2018 16:39
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  • Nov 21 2018 11:15
    ewels commented #39
  • Nov 20 2018 23:23
    lutsik commented #39
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    ewels commented #39
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    lutsik commented #39
  • Nov 08 2018 13:08
    ebete starred ewels/MegaQC
  • Oct 17 2018 13:26
    tsnowlan commented #70
  • Oct 11 2018 14:09
    ewels commented #67
  • Oct 11 2018 12:06
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  • Oct 10 2018 15:14
    ewels labeled #70
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  • Oct 10 2018 11:23
    ewels commented #69
  • Oct 10 2018 11:09
    tsnowlan commented #69
  • Oct 10 2018 10:06
    ewels commented #68
  • Oct 10 2018 10:05

    ewels on FLASK_DEBUG

    (compare)

Phil Ewels
@ewels
Ah, and it’s definitely a recent version of MultiQC?
The code that triggers that message isn’t doing anything particularly special: https://github.com/ewels/MegaQC/blob/master/megaqc/commands.py#L173
Sehrish Kanwal
@skanwal

Ah, that’s going to be interesting.

which multiqc > /Users/kanwals/miniconda3/envs/multiqc/bin/multiqc
which megaqc > /Users/Kanwals/miniconda3/bin//megaqc

As you can tell, I installed both tools in separate conda environment. Aslo, used pip for megaqc installation.
Should I try installing megaqc in multiqc environment.?
Multiqc version is 1.7, so should definitely be not an issue.

Phil Ewels
@ewels
Yes they need to be installed in the same environment
Otherwise they are using different python installations, so they can’t see each other
Pip installs within a conda environment should be fine
which pip should show it in the conda env.
Sehrish Kanwal
@skanwal

Phil, tried reinstalling megaQC in the multiQC conda environment using pip. The installation went okay.
Both the tools are now installed in the same environment.
which megaqc > /Users/kanwals/miniconda3/envs/multiqc/bin/megaqc
which multiqc > /Users/kanwals/miniconda3/envs/multiqc/bin/multiqc

For testing, ran multiqc on a sample, and the report was successfully posted to megaqc server.
But upload is again throwing the same issue:

megaqc upload multiqc_data/multiqc_data.json
This is MegaQC v0.1.dev1

Env: test
 * Database type: sqlite
 * Database path: sqlite:////Users/kanwals/miniconda3/lib/python3.6/site-packages/test.db
Error - This function requires MultiQC to be installed
Phil Ewels
@ewels
Strange. Could you make an issue about this on the GitHub repo please?
I have no ideas as to how or why this could happen now though
It’s nothing special about MegaQC or MultiQC here - it’s just a simple python import.
Sehrish Kanwal
@skanwal
Thanks, Phil.
Sure, I'll open an issue on GitHub.
Michael Milton
@TMiguelT
I'd appreciate feedback from anyone on my Dash integration PR: ewels/MegaQC#81
Michael Milton
@TMiguelT
@ewels if you can get back to me about the dash PR and also the control chart thresholds, that would be great
I have an upcoming meeting at my work where I'll be talking about MegaQC, and if I can implement and then show off some of these features, there's a much better chance I'll be given time to work on MegaQC
Michael Milton
@TMiguelT
In particular I want to implement something for the alert thresholds that I can show, but I want to know if Dash is a reasonable direction to be taking
Phil Ewels
@ewels
I'll do my best :+1:
Michael Milton
@TMiguelT
Much appreciated
Michael Milton
@TMiguelT
Can you explain why the MegaQC API uses a token, rather than just the session cookies that normal requests use?
Phil Ewels
@ewels
Not sure I remember sorry.
I guess you don’t mean the key pair for uploads? Just regular API calls in-page?
That code was nearly all written by Denis (who changed jobs right after), so I don’t have a lot of insight into it sorry
Michael Milton
@TMiguelT
I mean the API token used for API calls from JavaScript
It's unusual because the application authenticates the user login, and then sets a session cookie. But then it also gives the user an API token which to me seems redundant
Phil Ewels
@ewels
Probably is then :+1: