Database and FTP setup

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Database and FTP setup

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 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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Database and ftp setup

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 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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Re: Database and FTP setup

Nate Coraor (nate@bx.psu.edu)
In reply to this post by Conrad, Turner Allen
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 <[hidden email]> 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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Re: Database and FTP setup

Conrad, Turner Allen
In reply to this post by Conrad, Turner Allen
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: [hidden email]
Office: (210) 567-3947
Cell: (210) 954-0893

On Feb 20, 2014 10:23 PM, Nate Coraor <[hidden email]> 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 <[hidden email]> 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
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>
>

___________________________________________________________
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in your mail client.  To manage your subscriptions to this
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Re: Database and FTP setup

Nate Coraor (nate@bx.psu.edu)
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) 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                  [hidden email] dbuser dbpassword
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,'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 <[hidden email]> 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: [hidden email]
Office: <a href="tel:%28210%29%20567-3947" value="+12105673947">(210) 567-3947
Cell: <a href="tel:%28210%29%20954-0893" value="+12109540893">(210) 954-0893

On Feb 20, 2014 10:23 PM, Nate Coraor <[hidden email]> 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 <[hidden email]> 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
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>
>


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/