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

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Helena Rasche
@hexylena:matrix.org
[m]
for multiple terminals you can use ctrl-a c to open a new 'tab'
and then ctrl-a n and ctrl-a p to go between them @lldelisle
Lucille Delisle
@lldelisle
I just found your help for byobu
Helena Rasche
@hexylena:matrix.org
[m]
ahh good :)
Lucille Delisle
@lldelisle
For port 21, should I ask Mauro for another VM with port 21 opened?
Helena Rasche
@hexylena:matrix.org
[m]
or set it to a different port?
50k-60k are available.
Lucille Delisle
@lldelisle
OK I will try tomorrow.
Thanks
Helena Rasche
@hexylena:matrix.org
[m]
(you can of course! but since you've already got this VM setup, it would take less time to just make the configuration use a different port for writing the tutorial, and we can change it after.)
Lucille Delisle
@lldelisle

Good morning. I used 55k as Port but it does not appear from outside:

$ nmap gat-79.be.training.galaxyproject.eu
Starting Nmap 7.91 ( https://nmap.org ) at 2021-06-18 09:24 CEST
Nmap scan report for gat-79.be.training.galaxyproject.eu (193.190.80.99)
Host is up (0.022s latency).
rDNS record for 193.190.80.99: t1cl0128.guest.ugent.be
Not shown: 992 filtered ports
PORT     STATE  SERVICE
22/tcp   open   ssh
80/tcp   open   http
113/tcp  closed ident
443/tcp  open   https
2000/tcp open   cisco-sccp
5060/tcp open   sip
8008/tcp open   http
8080/tcp open   http-proxy

Nmap done: 1 IP address (1 host up) scanned in 4.89 seconds

When I try to connect with lftp from outside to the port I set (55k). I get a Connection time out. I don't know anything about port but I have the feeling that I need a command port smaller than 1023.

Helena Rasche
@hexylena:matrix.org
[m]
yeah, confirmed locally that it's not getting through.
less than 1024 shouldn't matter, the only thing special there is they require root to access.
Lucille Delisle
@lldelisle
ok
Helena Rasche
@hexylena:matrix.org
[m]
I think I know what it is
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.