Question: error for ftp set up for local galaxy instance
gravatar for yychangsd
2.3 years ago by
yychangsd30 wrote:

I install postgresql and proftpd

and modified galaxy.ini like this

port = 8080 host = filter-with = gzip use_interactive = False debug = False cleanup_job = onsuccess Switching to PostgreSQL database server ftp_upload_dir = ftp_upload_site = localhost:2021

It works well but no ftp shown in upload window.

Then I add this in galaxy.ini database_connection = galaxy:1Galaxy@localhost:5432/galaxy_db

It showed that after sh

galaxy.queue_worker INFO 2016-08-16 23:05:12,086 Initializing main Galaxy Queue Worker on sqlalchemy+galaxy:1Galaxy@

gaierror: [Errno -2] Name or service not known

I already set up a galaxy_db with username galaxy and password !Galaxy in postgresql

So any help would be appreciated~~


galaxy • 558 views
ADD COMMENTlink modified 2.3 years ago by Devon Ryan1.9k • written 2.3 years ago by yychangsd30
gravatar for Devon Ryan
2.3 years ago by
Devon Ryan1.9k
Devon Ryan1.9k wrote:

Your post isn't rendering correctly (put things like the configuration in a code block).

Anyway, you need to set ftp_upload_dir to a path, such as /export/galaxy-central/database/ftp, and proftpd needs to know to put things there.

BTW, you probably want database_connection = postgresql://galaxy:1Galaxy@localhost:5432/galaxy_db

ADD COMMENTlink written 2.3 years ago by Devon Ryan1.9k

Thanks for your help. It starts well and I can check it from the server, but still no "choose ftp file" shown in upload file windows. Maybe it is because I did not tell proftpd to put things in the desired folder. Would you please tell me how to do it? Thanks~~

ADD REPLYlink written 2.3 years ago by yychangsd30

Below is the end of the proftpd.conf file that setup inside docker instances of Galaxy by ansible

# Do not authenticate against real (system) users
AuthPAM                         off

# Set up mod_sql_password - Galaxy passwords are stored as hex-encoded SHA1
SQLPasswordEngine               on
SQLPasswordEncoding             hex

# Set up mod_sql to authenticate against the Galaxy database
SQLEngine                       on
SQLBackend                      postgres
SQLConnectInfo                  galaxy@localhost galaxy galaxy
SQLAuthTypes                    SHA1
SQLAuthenticate                 users

# An empty directory in case chroot fails
SQLDefaultHomedir               /var/opt/local/proftpd

# Define a custom query for lookup that returns a passwd-like entry.  UID and GID should match your Galaxy user.
SQLUserInfo                     custom:/LookupGalaxyUser
SQLNamedQuery                   LookupGalaxyUser SELECT "email,password,'%{env:GALAXY_UID}','%{env:GALAXY_GID}','/export/galaxy-central/database/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U'"
ADD REPLYlink written 2.3 years ago by Devon Ryan1.9k

Thanks, it works. but now get an new error in my anther post: can not log in FTP server at localhost:2021

ADD REPLYlink written 2.3 years ago by yychangsd30
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