Re: [galaxy-dev] Database and FTP setup
Thanks, Nate! Got it to run after playing with the postgresql url, table was created, and I began populating it with my admin account. I also prepared the database for ftp by creating a user for lookup. As for proftpd, I have it installed, but am not quite sure what do now. How must I edit the postgresql and proftpd configuration files before changing the galaxy ini? ---------------------------------------------------- 1LT Turner A Conrad, USAR IRR Ph.D. Candidate Graduate School of Biomedical Sciences MED 4.017V Dept. of Microbiology and Immunology 7703 Floyd Curl Drive San Antonio, TX 78229 Email: conradt@livemail.uthscsa.edu Office: (210) 567-3947 Cell: (210) 954-0893 On Feb 20, 2014 10:23 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Hi Turner,
You should be connecting to the database that Galaxy is using, specified in the database_connection option in universe_wsgi.ini. If you have not yet started Galaxy at least once, then the tables will not have been created yet. Once you run Galaxy and the tables have been created, you should be able to connect to that database (galaxydb, or whatever you have set in database_connection) with psql and the GRANT should succeed.
--nate
On Thu, Feb 20, 2014 at 9:49 AM, Conrad, Turner Allen <ConradT@livemail.uthscsa.edu> wrote:
Hi,
I'm not experienced with postgres and ftp and am thus having difficulties setting up an ftp server on my local Galaxy instance, but it is essential as our files are all over 2GB. The admin support page (https://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP) is a little fuzzy on the details. I'm currently running the server out of Ubuntu 13.10 desktop both physically and via SSH. So far, I've created a local account postgres with a psql database galaxydb and user galaxyftp, but I can't figure out whether the galaxy_user table is supposed to exist, needs to be created, nor how to add this information to the database_connection option in universe_wsgi.ini. ALTER ROLE has been completed successfully, but I get the error ERROR: relation "galaxy_user" does not exist upon attempting GRANT SELECT ON. Is there a simple explanation of how to complete this task and get the proftpd server up and running for Ubuntu? Please assume proftpd is installed, but not configured, the database is in the state described above, and I am starting with sudo su - postgres followed by psql galaxydb .
Turner Conrad UTHSCSA
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Hi Turner, In universe_wsgi.ini, set 'use_pbkdf2 = False' in the '[app:main]' section. You probably do not need to make any changes to PostgreSQL's configuration unless your database is running on a different host from your Galaxy server. For proftpd.conf, the most important bits are these: # Do not authenticate against real (system) usersAuthPAM off# Set up mod_sql_password - Galaxy passwords are stored as hex-encoded SHA1SQLPasswordEngine onSQLPasswordEncoding hex# Set up mod_sql to authenticate against the Galaxy databaseSQLEngine onSQLBackend postgresSQLConnectInfo galaxydb@dbserver.example.org dbuser dbpasswordSQLAuthTypes SHA1SQLAuthenticate users# An empty directory in case chroot failsSQLDefaultHomedir /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:/LookupGalaxyUserSQLNamedQuery LookupGalaxyUser SELECT "email,password,'512','512','/home/nate/galaxy_dist/database/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U'" In your instance you most likely want: SQLConnectInfo galaxydb@/var/run/postgresql galaxyftp galaxyftpUsersPassword In SQLNamedQuery, make sure that you change the first 512 to the uid of the system user id your Galaxy server is running as, and the second 512 to the system group id. These can be obtained with `id -u` and `id -g` on the command line. /home/nate/galaxy_dist/database/ftp should be changed to the directory on your server in which files uploaded via FTP should be placed (this location is not permanent - the files themselves will be copied into the Galaxy directory). Hope this helps, --nate On Thu, Feb 20, 2014 at 11:33 PM, Conrad, Turner Allen < ConradT@livemail.uthscsa.edu> wrote:
Thanks, Nate! Got it to run after playing with the postgresql url, table was created, and I began populating it with my admin account. I also prepared the database for ftp by creating a user for lookup. As for proftpd, I have it installed, but am not quite sure what do now. How must I edit the postgresql and proftpd configuration files before changing the galaxy ini?
---------------------------------------------------- 1LT Turner A Conrad, USAR IRR Ph.D. Candidate Graduate School of Biomedical Sciences
MED 4.017V Dept. of Microbiology and Immunology 7703 Floyd Curl Drive San Antonio, TX 78229
Email: conradt@livemail.uthscsa.edu Office: (210) 567-3947 Cell: (210) 954-0893
On Feb 20, 2014 10:23 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Hi Turner,
You should be connecting to the database that Galaxy is using, specified
in the database_connection option in universe_wsgi.ini. If you have not yet started Galaxy at least once, then the tables will not have been created yet. Once you run Galaxy and the tables have been created, you should be able to connect to that database (galaxydb, or whatever you have set in database_connection) with psql and the GRANT should succeed.
--nate
On Thu, Feb 20, 2014 at 9:49 AM, Conrad, Turner Allen <
Hi,
I'm not experienced with postgres and ftp and am thus having
difficulties setting up an ftp server on my local Galaxy instance, but it is essential as our files are all over 2GB. The admin support page ( https://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP) is a
ConradT@livemail.uthscsa.edu> wrote: little fuzzy on the details. I'm currently running the server out of Ubuntu 13.10 desktop both physically and via SSH. So far, I've created a local account postgres with a psql database galaxydb and user galaxyftp, but I can't figure out whether the galaxy_user table is supposed to exist, needs to be created, nor how to add this information to the database_connection option in universe_wsgi.ini. ALTER ROLE has been completed successfully, but I get the error ERROR: relation "galaxy_user" does not exist upon attempting GRANT SELECT ON. Is there a simple explanation of how to complete this task and get the proftpd server up and running for Ubuntu? Please assume proftpd is installed, but not configured, the database is in the state described above, and I am starting with sudo su - postgres followed by psql galaxydb .
Turner Conrad UTHSCSA
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Nate Coraor