Question: No "Files uploaded via FTP" option in local Galaxy instance
0
gravatar for gbot300
3.1 years ago by
gbot3000
South Africa
gbot3000 wrote:

Hi Guys

We run a local Galaxy instance. I've followed the https://wiki.galaxyproject.org/Admin/Config/UploadviaFTP tut and have managed to get everything working successfully using PROFTPD and MYSQL. Files are transferred successfully via the FTP client and appear in the desired directory with the correct permissions.

The only part that's missing is that the "Files uploaded via FTP" option is not being presented to my user in the Upload File form interface. Any clues as to what I missed?

Thanx a lot and great product!

gordon

mysql proftpd ftp galaxy • 1.3k views
ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by gbot3000
0
gravatar for Daniel Blankenberg
3.1 years ago by
Daniel Blankenberg ♦♦ 1.7k
United States
Daniel Blankenberg ♦♦ 1.7k wrote:

Hi Gordon, have you been sure to configure these options in your galaxy.ini file?

 

# Enable Galaxy's "Upload via FTP" interface.  You'll need to install and
# configure an FTP server (we've used ProFTPd since it can use Galaxy's
# database for authentication) and set the following two options.

# This should point to a directory containing subdirectories matching users'
# email addresses, where Galaxy will look for files.
#ftp_upload_dir = None

# This should be the hostname of your FTP server, which will be provided to
# users in the help text.
#ftp_upload_site = None
ADD COMMENTlink written 3.1 years ago by Daniel Blankenberg ♦♦ 1.7k

In am trying to utilize Galaxy server in ubuntu 16 based system .

It works perfectly, but i am not able to list the ftp files uploaded to the server. I have already set both the configuration as discussed above, but unfortunately, it is not working for me.

Please help me to resolve this problem.

# Enable Galaxy's "Upload via FTP" interface.  You'll need to install and
# configure an FTP server (we've used ProFTPd since it can use Galaxy's
# database for authentication) and set the following two options.

# This should point to a directory containing subdirectories matching users'
# identifier (defaults to e-mail), where Galaxy will look for files. 
ftp_upload_dir = /home/vishal/galaxy/database/files

# This should be the hostname of your FTP server, which will be provided to
# users in the help text. 
ftp_upload_site = galaxy

# User attribute to use as subdirectory in calculating default ftp_upload_dir
# pattern. By default this will be email so a user's FTP upload directory will be
# ${ftp_upload_dir}/${user.email}. Can set this to other attributes such as id or
# username though.
#ftp_upload_dir_identifier = email

Screenshot of upload menu

ADD REPLYlink modified 7 months ago • written 7 months ago by vmevada1020
0
gravatar for gbot300
3.1 years ago by
gbot3000
South Africa
gbot3000 wrote:

Hi Daniel

We were using the "old" [galaxy:tool_runners] format for setting job runner configurations. The old format wasn't being read correctly, which caused the FTP settings, which are basically sequential in the galaxy.ini file, to also be read incorrectly. From looking at the logs it seems that the FTP settings were also being interpreted as job_runner configurations, so I suspect we're not defining the end of the [galaxy:tool_runners]  section correctly.

Anyhow, FTP uploads is working perfectly now and I am redoing the job runner settings in the new job_conf.xml format. Should be fine from here.

Thanx!

g

ADD COMMENTlink written 3.1 years ago by gbot3000
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