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  • Jan 31 2019 22:37

    bebatut on gh-pages

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    erasche on master

    Reports fix. Clear up issue in Galaxy docker… More reports fixes... and 1 more (compare)

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    fix typos Merge pull request #1236 from g… (compare)

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    martenson on martenson-patch-2

    fix typos (compare)

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Lucille Delisle
@lldelisle
Ah
Helena Rasche
@hexylena:matrix.org
[m]
there's two levels of firewalling going on; one from the cloud, and then one from their network guys on top of it.
the cloud we can change. The network folks, no. We will not be getting any more ports.
Lucille Delisle
@lldelisle
ok
Helena Rasche
@hexylena:matrix.org
[m]
let me try making a change quickly
Lucille Delisle
@lldelisle
OK but don't spend too much time. It is not a problem to setup a new machine if it is easier.
Helena Rasche
@hexylena:matrix.org
[m]
nah it's just a firewall change, it'll take 5 min
Helena Rasche
@hexylena:matrix.org
[m]
fixed
Lucille Delisle
@lldelisle
You're the best.
Lucille Delisle
@lldelisle

Sorry to bother you again. I managed to upload a file into the ftp. I set up the ftp_upload_dir:

$ cat /srv/galaxy/config/galaxy.yml  | grep ftp
    ftp_upload_dir: /uploads

But in the user web interface in the upload I cannot see the "ftp" button...

image.png
Helena Rasche
@hexylena:matrix.org
[m]
hmm
it doesn't look like it restarted by the systemd times
ubuntu@gat-79:/srv/galaxy$ systemctl status galaxy
● galaxy.service - Galaxy
     Loaded: loaded (/etc/systemd/system/galaxy.service; enabled; vendor preset: enabled)
     Active: active (running) since Fri 2021-06-18 07:53:07 UTC; 18min ago
did it not trigger a restart when you changed the conf file?
(or maybe that restart was when you changed it)
anyway
I don't know, unexpected!
Lucille Delisle
@lldelisle
But I restarted it manually...
Just in case...
$ sudo systemctl restart galaxy
Helena Rasche
@hexylena:matrix.org
[m]
ah damn
try setting the other vars? ftp_upload_site? maybe one of those triggers it
Lucille Delisle
@lldelisle
OK
Helena Rasche
@hexylena:matrix.org
[m]
yeah I think that'll do it
Lucille Delisle
@lldelisle
Yes
It worked.
I think the doc needs to be updated because it is misleading.
1 reply
Helena Rasche
@hexylena:matrix.org
[m]
$ curl --silent https://gat-79.be.training.galaxyproject.eu/api/configuration -k | jq | grep ftp
  "ftp_upload_site": null,
the only ftp var in the configuration dict is ftp_upload_site, and I only see ftp_upload_site in the client dir
very misleading!
Lucille Delisle
@lldelisle
Yes
Helena Rasche
@hexylena:matrix.org
[m]
perfect :)
Lucille Delisle
@lldelisle
I am so happy that I managed to make it work... Thank you so much for the help
1 reply
Helena Rasche
@hexylena:matrix.org
[m]
not sure if you're familiar with how the config schema has changed in recent years, but in case anyone else isn't, now we update lib/galaxy/webapps/galaxy/config_schema.yml and run make config-rebuild to keep galaxy.yml.sample up to date.
Lucille Delisle
@lldelisle
I am absolutely not. Thanks
Helena Rasche
@hexylena:matrix.org
[m]
@lldelisle: this tutorial looks fantastic, I did not expect this!
I'll review it today then
"first version", pff, this is basically mergeable as is :)
Lucille Delisle
@lldelisle
I feel like I am filling this chat... Sorry.
Why the tools are clickable from GTN in usegalaxy.eu/org/.org.au and not .be/my local instance? Is there a variable to set?
Helena Rasche
@hexylena:matrix.org
[m]
no worries
it should be mentioned at the bottom of the frame "Click to run unavialble" or so
you need to setup some proxying for it to work
Lucille Delisle
@lldelisle
Thanks I should better read git-gat.
pvanheus
@pvanheus
in the tutorial I'm writing at the moment I have an "Advanced" section on using the Rule Base Uploader instead of setting up collections manually. Is there a way to collapse this and only have it show if the reader clicks on something?
Saskia Hiltemann
@shiltemann:matrix.org
[m]
Make it a tip type box ?
pvanheus
@pvanheus
ok I'll have a look at how that renders...
Ana Sosa
@AnaSF_gitlab
Hello, can I ask if someone has gone through the Reference-based RNA-Seq data analysis training?
Saskia Hiltemann
@shiltemann
@AnaSF_gitlab go for it!
Ana Sosa
@AnaSF_gitlab
@shiltemann heh thanks, I'm on it :) I got an error and not sure how to proceed. so I'm wondering if someone is familiar with this training