FTP questions

[lecorguille]

Hi,

RRooowww, it seems really simple but I can't figure out why I can't upload file using FTP.

Note that I'm using a Mac

I launch that:
docker run -d -p 8080:80 -p 8021:21 -v ~/tmp/galaxy_docker_export:/export/ bgruening/galaxy-stable

I register within the galaxy instance accessible via http://127.0.0.1:8080

I tried that:

$ ftp [email protected] 8021
Connected to 127.0.0.1.
220 ProFTPD 1.3.5rc3 Server (Public Galaxy FTP) [::ffff:172.17.0.2]
331 Password required for lecorguille
Password:
530 Login incorrect.

The FTP folder is there:
/export/galaxy-central/database/ftp/[email protected]

Is there something I missed? Can you point me a log file within the container because I got nothing in /var/log/proftpd?

Many many thanks!

[bgruening]

Can this be an issue with the passive mode? https://github.com/bgruening/docker-galaxy-stable#using-passive-mode-ftp

[mvdbeek]

$ ftp [email protected] 8021
Connected to 127.0.0.1.
220 ProFTPD 1.3.5rc3 Server (Public Galaxy FTP) [::ffff:172.17.0.2]
331 Password required for lecorguille
Password:
530 Login incorrect.

You have to use your email address that you have used to register in galaxy, I'm afraid username alone is not enough. But you'll also be facing problems with passive mode on a mac, as bjoern pointed out. If this is just your local machine, you can copy files into the ftp folder, they will appear in the upload box even without using FTP.

[lecorguille]

@bgruening
I tried --net=hostbut I can't reach using htpp://127.0.0.1

CONTAINER ID        IMAGE                     COMMAND              CREATED             STATUS              PORTS                                                            NAMES
d06664228146        bgruening/galaxy-stable   "/usr/bin/startup"   7 minutes ago       Up 7 minutes                                                                         drunk_jennings

and the logs gave:

Starting ProFTP
proftpd: ERROR (abnormal termination)

==> /home/galaxy/logs/slurmd.log <==
[2016-08-09T09:05:04.507] error: Unable to resolve "moby": Unknown host
[2016-08-09T09:05:04.507] error: Unable to establish control machine address
[2016-08-09T09:05:04.507] error: Unable to register: No error
[2016-08-09T09:05:05.510] error: Unable to resolve "moby": Unknown host
[2016-08-09T09:05:05.510] error: Unable to establish control machine address
[2016-08-09T09:05:05.510] error: Unable to register: No error
[2016-08-09T09:05:06.513] error: Unable to resolve "moby": Unknown host
[2016-08-09T09:05:06.513] error: Unable to establish control machine address
[2016-08-09T09:05:06.513] error: Unable to register: No error
[2016-08-09T09:05:07.518] error: Unable to resolve "moby": Unknown host
[...]

@mvdbeek
Until now, I always use the "Public name" in our production instance.
CyberDuck don't like [email protected]@127.0.0.1
Using the CLI, I tried with ftp 127.0.0.1 8021 and then lecorguille@sb-roscoff: I managed to estabish a connection ... in passive mode

I tested that because we are close to propose a Galaxy flavor and I wanted to propose a quick-start. I will try using the "Docker toolbox" instead of the new "Docker for Mac"

[mvdbeek]

@lecorguille if you want to use --net=host you'll have to use the IP address of the hypervisor, because unlike on linux the docker host is not localhost ... I haven't figured how to do that with docker for mac, but this is possible with with docker machine or the docker toolbox.

Using the CLI, I tried with ftp 127.0.0.1 8021 and then lecorguille@sb-roscoff: I managed to estabish a connection ... in passive mode

Yeah, but have you tried to list or copy files? Because passive mode will need additional high ports for transfer, and those are not exposed.

[lecorguille]

• MacOSX + Docker for Mac + -p 8021:21 + user = 👎
• MacOSX + Docker for Mac + -p 8021:21 + user.email = 👎
• MacOSX + Docker for Mac + --net=host + user.email = 👎
• MacOSX + Docker Toolbox + --net=host + user.email = 👍
• MacOSX + Docker Toolbox + --net=host + user.public_name = 👎
• MacOSX + Docker Toolbox + --net=host + user.email = 👍

Thank you guys

My next problem is about /export

• MacOSX + Docker Toolbox + /export = 👎

lecorguille@MacBook ~ $ docker logs -f foobar
Starting ProFTP
proftpd: started
Starting Galaxy reports webapp
reports: ERROR (abnormal termination)
Starting nodejs
galaxy:galaxy_nodejs_proxy: ERROR (abnormal termination)

[...]

==> /home/galaxy/logs/uwsgi.log <==
  File "lib/galaxy/webapps/galaxy/buildapp.py", line 63, in paste_app_factory
    app = galaxy.app.UniverseApplication( global_conf=global_conf, **kwargs )
  File "lib/galaxy/app.py", line 54, in __init__
    self.config.check()
  File "lib/galaxy/config.py", line 650, in check
    self._ensure_directory( path )
  File "lib/galaxy/config.py", line 631, in _ensure_directory
    raise ConfigurationError( "Unable to create missing directory: %s\n%s" % ( path, e ) )
ConfigurationError: Unable to create missing directory: /export/galaxy-central/database/files
[Errno 13] Permission denied: '/export/galaxy-central/database'

lecorguille@MacBook ~ $ docker exec -it foobar /bin/bash
root@default:/galaxy-central# su galaxy
galaxy@default:/galaxy-central$ touch /export/yo
touch: cannot touch ‘/export/yo’: Permission denied

• MacOSX + Docker for Mac + /export = 👍

lecorguille@MacBook ~ $ docker exec -it foobar /bin/bash
root@39122946cb0d:/galaxy-central# su galaxy
galaxy@39122946cb0d:/galaxy-central$ touch /export/yo

[bgruening]

Oh Docker on Mac ... any chance you can use a Linux ;)

MacOSX + Docker Toolbox + /export = 👎

This is probably because of the OSX file system. Please refer to the data-volumes section here to get it working: https://github.com/bgruening/docker-galaxy-stable#usage
We have one Galaxy instance running in Stuttgart with data-volumes.

[lecorguille]

There is also this project I found somewhere: https://github.com/codekitchen/dinghy
I didn't test yet.

[bgruening]

@lecorguille as an alternative can you please try if #217 works for you?

[bgruening]

@lecorguille please try sftp if OSX is playing the Diva ;) and feel free to reopen if necessary.

[lecorguille]

Hi,

Sorry @bgruening, I'm curently on hollyday. I will update this thread and
other ASAP.
Meanwhile, thank you !
Cheers
Le 25 août 2016 08:54, "Björn Grüning" [email protected] a écrit :

Closed #210 #210
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[lecorguille]

OK, it works when I use the command line and Filezilla but fails with Cyberduck.
I get Broken transport; encountered EOF.

But Filezilla is enough for me to check the container.

So thanks you!

[bgruening]

Thanks for getting back to me!