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  • Feb 15 09:42
    gedankenstuecke commented #534
  • Feb 12 07:04
    apriha opened #534
  • Oct 29 2020 12:57
    CholoTook commented #460
  • Oct 29 2020 12:42
    gedankenstuecke commented #460
  • Oct 29 2020 11:34
    CholoTook commented #460
  • Sep 22 2020 03:07
    apriha commented #533
  • Sep 21 2020 14:52

    gedankenstuecke on master

    Add link to `snps` library (#53… (compare)

  • Sep 21 2020 14:52
    gedankenstuecke closed #533
  • Sep 21 2020 14:52
    gedankenstuecke commented #533
  • Sep 21 2020 04:58
    apriha opened #533
  • Sep 21 2020 04:52
    Travis apriha/snpr@38f66d2 (add-link-to-snps) passed (1)
  • Jul 28 2020 08:49

    tsujigiri on update-rack

    (compare)

  • Jul 28 2020 08:49

    tsujigiri on master

    Update rails (#532) (compare)

  • Jul 28 2020 08:49
    tsujigiri closed #532
  • Jul 28 2020 08:21
    tsujigiri opened #532
  • Jul 28 2020 08:20
    Travis openSNP/snpr@8c512ff (update-rack) passed (2327)
  • Jul 28 2020 08:17

    tsujigiri on update-rack

    Update rails (compare)

  • Jul 28 2020 07:13

    tsujigiri on bundler

    (compare)

  • Jul 28 2020 07:13

    tsujigiri on master

    Bump json from 2.1.0 to 2.3.0 (… (compare)

  • Jul 28 2020 07:13
    tsujigiri closed #531
Philipp Bayer
@philippbayer
nice, i just resubmitted a paper on Amborella pangenomics
Amborella
@Amborella
Yeah, I think Amborella is amazing. Strongly considering taking a holiday in New Caledonia sometime in the next few years just so I can get myself a pot of the stuff and bring it back. Although I'm more interested in it from the rare plant side of things than the genetics side.
Bastian Greshake Tzovaras
@gedankenstuecke
All the best for the resubmission!
Sina Rüeger
@sinarueeger
Hi, for some reason the SSL certificate expired again, could you update that?
Philipp Bayer
@philippbayer
sorry about that, fixing it right now
done!
Sina Rüeger
@sinarueeger
many thanks!
Philipp Bayer
@philippbayer
@gedankenstuecke @tsujigiri i've just added a bash script to /root/run-letsencrypt.sh and added that to crontab, let's see whether that works :PP
the current cert expires Sunday, 22 November 2020. if it works right then next thursday (tomrorow) we'll have a later cert.
Helge Rausch
@tsujigiri
I already added a CRON job earlier. Doesn't seem to work... :laughing:
Helge Rausch
@tsujigiri
0 0 * * * root /usr/local/bin/renew_ssl_cert.sh
Bastian Greshake Tzovaras
@gedankenstuecke
😂
Is it because something needs to be run as app instead of root for the containers?
Philipp Bayer
@philippbayer
is yours running within the container? mine's running on the host OS
Bastian Greshake Tzovaras
@gedankenstuecke
Yeah, but I remember that there used to be some issue if you tried to do things inside the host OS if the stuff was owned by the container
Helge Rausch
@tsujigiri
Yes, it's running inside the container.
From the logs it seems to be running, but there is no output, good or bad...
I changed it to 0 0 * * * root /usr/local/bin/renew_ssl_cert.sh > /var/log/renew_ssl_cert.log 2>&1 now, let's see...
Helge Rausch
@tsujigiri
Plenty of time to renew, exiting.
I remember seeing this the last time I checked. I'll change the Dockerfile to permanently log the output, so we see what happens over time...
Bastian Greshake Tzovaras
@gedankenstuecke
Great, thanks!
Philipp Bayer
@philippbayer
thanks :) I see my bad script is commented out, good so they don't clash
Philipp Bayer
@philippbayer
the ssl cert is still until the 22. november
Helge Rausch
@tsujigiri
When I run it, it still says Plenty of time to renew, exiting. No sure when it decides its close enough. There is also openSNP/opensnp.org-docker#18 still open.
Philipp Bayer
@philippbayer
thanks, merged!
yes normally when we run it manually we're too late ^^
Philipp Bayer
@philippbayer
hmmmm cert still expires 22.11.2020
i.e., the old one
Helge Rausch
@tsujigiri
I think it allows renewal one month before expiration, at the earliest. Maybe even less.
Chill! :smile:
Maybe we should subscribe to the notification emails? https://letsencrypt.org/docs/expiration-emails/
Bastian Greshake Tzovaras
@gedankenstuecke
that sounds good, at least we get an early warning if the cronjob fails :D
sk75
@sk75
Is it possible or is this available .. I'm looking for SNP data that represent a family over a few generations. Is it readily available as one download. Or how can I search and make up a set of SNPs. Any help is appreciated, apologies if this is not the right question for here, and if the question does not make much sense as I just am starting to get interested in this.
Sharif Islam
@sharifX
I recently downloaded opensnp dataset. I need to store the genotype_frequency data for each rsid. This was not in the download. Is there a way to get this data downloaded (without calling the JSON endpoint)?
Bastian Greshake Tzovaras
@gedankenstuecke
@sharifX sorry for the delay in answering, it was grant writing season in France! Unfortunately there’s no easy way to get the frequencies for each rsid without downloading the whole data set and calculating them yourself at this point
VittorioAccomazzi
@VittorioAccomazzi

@sharifX @gedankenstuecke I faced a similar problem with my 23andme data. So I wrote an application for it, which display the frequency for the MT and Y Chromosomes (I’m interested mostly in genealogy). It is a web app, and processes the data is your browser:
https://vittorioaccomazzi.github.io/snpsandme/
The application displays the frequency of each rsid using the dbSNP and then sorts them.It also provides link and number of publications. So it allows to explore your genome easily, with the support of dbSNP.

The source code is on github. 🖐 Feedback is welcome !

Bastian Greshake Tzovaras
@gedankenstuecke
@VittorioAccomazzi thanks for sharing! For me it ends up with a blank page and the JS console throws an error in GA4React :)
VittorioAccomazzi
@VittorioAccomazzi
@gedankenstuecke which browser are you using ? If you don't mind I would like to understand what is happening. I validated on Chrome, Edge and Safari
Bastian Greshake Tzovaras
@gedankenstuecke
I tried in both Chrome and Firefox
VittorioAccomazzi
@VittorioAccomazzi
@gedankenstuecke the error reported by GA4React says "ga4manager.tsx:182 Uncaught (in promise) Error: GA4React Timeout" followed by "at ga4manager.tsx:182" ?
Bastian Greshake Tzovaras
@gedankenstuecke
Yep
VittorioAccomazzi
@VittorioAccomazzi
@gedankenstuecke Thank you. I increased the timeout. I appreciate if you can retry and let me know: https://vittorioaccomazzi.github.io/snpsandme/ .Hopefully it will work this time. In any case in this video you can see how the application works : https://www.youtube.com/watch?v=lUS8Q2-EbyY . In short the application displays the SNPs of the Y and MT chromosome and sort them by frequency. For each SNP it reports the number of publication and links to dbSNP, so you can navigate quickly your genome.
Bastian Greshake Tzovaras
@gedankenstuecke
@VittorioAccomazzi ah, nevermind! The problem was that the Google Tag Manager thing is blocked by adblockers by default and it couldn’t load anything because of that
it works now and is really cool!
VittorioAccomazzi
@VittorioAccomazzi
@gedankenstuecke thank you !
Philipp Bayer
@philippbayer
we're not affected by the docker business model changes, right?
Sina Rüeger
@sinarueeger
Hi, is it possible that the SSL certificate has expired?
Bastian Greshake Tzovaras
@gedankenstuecke
@sinarueeger it seems to work for me, but maybe the problem fixed itself since you sent your message? :)
Sina Rüeger
@sinarueeger

@gedankenstuecke indeed - I am now checking the examples you provide in the API description https://github.com/openSNP/snpr/wiki/JSON-API. All work when using a browser (only opensnp.org/snps/rs7903146.json is taking super long to appear - maybe this was always the case).

However, if I use R (curl and httr package) to query, it still gives me the SSL certificate expired error. Did you explicitly check if the SSL certificate is not expired?
I am not an API expert, so probably a problem on our end then.

Sidenote: Also if I click on "download dump" on https://opensnp.org/snps/ it leads to a 404.

Bastian Greshake Tzovaras
@gedankenstuecke
@sinarueeger i’ve kicked our server again for the dump, hopefully at the end of the day there’ll be a working one. For the API: does R maybe take some cached certificates? As I can’t see any issue with the certificate, it’s valid until december 17