Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
  • Jan 07 2019 15:05
    colindaven starred ewels/MegaQC
  • Dec 10 2018 16:46
    vzg100 starred ewels/MegaQC
  • Dec 10 2018 16:39
    sridhar0605 starred ewels/MegaQC
  • Nov 21 2018 11:15
    ewels commented #39
  • Nov 20 2018 23:23
    lutsik commented #39
  • Nov 20 2018 23:13
    ewels commented #39
  • Nov 20 2018 23:10
    lutsik commented #39
  • Nov 20 2018 22:59
    ewels commented #39
  • Nov 20 2018 22:27
    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
    shafqatb commented #67
  • Oct 10 2018 15:14
    ewels labeled #70
  • Oct 10 2018 15:14
    ewels labeled #70
  • Oct 10 2018 15:14
    ewels opened #70
  • 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)

Albert Vilella
@avilella
avilella@avilellaM710t:~/multiqc/test$ find $PWD/ -name "*.json" | xargs cat
{
    "report_general_stats_headers": [], 
    "config_version": "1.5dev", 
    "report_general_stats_data": [], 
    "config_creation_date": "2019-03-07, 16:48", 
    "config_title": null, 
    "config_report_comment": null, 
    "config_short_version": "1.5dev", 
    "config_intro_text": null, 
    "report_saved_raw_data": {}, 
    "report_data_sources": {}, 
    "report_multiqc_command": "/usr/local/bin/multiqc --force --filename /home/avilella/multiqc/test/report__multiqc /home/avilella/multiqc/test", 
    "config_analysis_dir": [
        "/home/avilella/multiqc/test"
    ], 
    "config_report_header_info": null, 
    "config_analysis_dir_abs": [
        "/home/avilella/multiqc/test"
    ], 
    "config_subtitle": null, 
    "report_plot_data": {}, 
    "config_script_path": "/usr/local/lib/python2.7/dist-packages/multiqc/utils", 
    "config_git_hash": null
}
avilella@avilellaM710t:~/multiqc/test$ cat *.txt
# plot_type: 'table'
# section_name: 'My section with a table'
# description: 'a custom text introduction (a few sentences) for this section'
# pconfig:
#     namespace: 'Cust Data'
# headers:
#     col1:
#         title: 'My Column'
#         description: 'This is a longer hover text for my column'
#         format: '{:,.0f}'
#     col2:
#         title: 'Second Column'
#         description: 'Hover description text'
Sample            col1            col2
samp_1            12.523          34
samp_2            56.947          78
avilella@avilellaM710t:~/multiqc/test$ #/usr/local/bin/multiqc --force --filename /home/avilella/multiqc/test/report__multiqc /home/avilella/multiqc/test
Phil Ewels
@ewels
Hmm, MultiQC v1.5dev
that's pretty old
we're on 1.8dev now
My guess is that you need to update MultiQC for this to work with custom content then
Albert Vilella
@avilella
I updated to 1.7 and it worked, thanks.
Phil Ewels
@ewels
Ok great!
Sehrish Kanwal
@skanwal

Hi Phil,
I am testing the megaqc upload function (locally on my laptop) to get data into megaQC server.
I am getting Error - This function requires MultiQC to be installed..
Following this issue on github https://github.com/ewels/MegaQC/issues/66, I have multiqc installed on my laptop and I am running the upload command from the same environment where I used multiqc to generate the report/json file.
For context, I installed multiqc via conda. The multiqc conda environment is also active in my session. Trying from multiqc.utils import config as multiqc_config on python interpreter also works fine..

Any idea what could be the underlying issue?

Phil Ewels
@ewels
Hi Sehrish - that sounds very odd!
Are you super-sure that everything is definitely in the same environment? By checking which megaqc and which multiqc..?
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
@multimeric
I'd appreciate feedback from anyone on my Dash integration PR: ewels/MegaQC#81
Michael Milton
@multimeric
@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
@multimeric
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
@multimeric
Much appreciated
Michael Milton
@multimeric
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
@multimeric
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:
Caspar
@caspargross
Hi! I need some help with setting up Reverse proxy for a public install of MegaQC. Everything is running (https://qc.imgag.de) but I get 405 error trying to upload data.
https://files.gitter.im/5af67ae0d73408ce4f99082b/HnWP/image.png
I think it is caused by running megaQC on localhost:8585 and only forwardig request to qc.imgag.de through the proxy. Here is my apache2 config:
image.png
Do you have any idea how to fix this setup?
Caspar
@caspargross
Figured it out! Was just the https redirect making things confusing. Uploading directly to https://qc.imgag.de works fine.
Phil Ewels
@ewels
Awesome! 👏🏻
Teemu Kuulasmaa
@kuulasmaa
I am new to MegaQC but this piece of software seems very promising, rough diamond I would say! I gave it a quick test drive and saw that there are some missing pieces and/or contains bugs. Yes, the project states very clearly that the current development status is "pretty unstable". May I ask that what kind of development plans do you have? And what do you think when MegaQC will be "production ready" or close to that? Basically I wondering whether I should start using, testing, debug, report bugs etc. now or should I look at some similar alternatives? I am not in hurry. If I just knew that MegaQC will be at more mature state (let say) at the end of this year I would be more than happy to commit to this project without looking any other alternatives.
Phil Ewels
@ewels
Hi @kuulasmaa ! Welcome :)
This project was started by me at SciLifeLab in Sweden and after an initial burst of development got a bit stale. We've had various attempts to get back into it and still harbour hopes to get properly stuck into it again, just not sure when.
Other sites have since adopted it and taken up the mantle of development however. Mostly @tsnowlan and @multimeric who have rewritten a lot of the code base now and contributed a lot of new features.
There are other groups also starting to pick it up as well, so I feel that especially recently the project is starting to pick up some momentum again, which is nice!
I can't say for sure when MegaQC will be considered production ready (it's already in production at several sites, so depends on your expectations and needs really!), but I can say that the project is active, if slow moving..
Phil Ewels
@ewels
And we'd love more users / contributors :)
Teemu Kuulasmaa
@kuulasmaa
Thank you for your quick response. I just wanted to make sure if this project is abandoned or not. "Production ready" was incorrect term. I am looking for something that is good/functional enough and there are at least some hope to see it improving in the future.
Michael Milton
@multimeric
It's not abandoned, and worth looking into, but really as Phil says the thing that would help the most is devs willing to help fix some of the bugs