Dear all,
I'm installing a local version of Galaxy but I'm having issues configuring the FTP upload functionality that I need. I assume the documentation in the wiki about configuring proftpd is outdated since Galaxy has recently changed authentication method. I apologize in advance for the length of this e-mail, thanks to everyone who will bother to reply.
My Galaxy set up uses Postgresql as db and nginx and it seems working fine. I installed the latest available version of Proftpd (1.3.5rc3) and compiled it with all the needed (I think) modules. Here they are:
mod_core.c mod_xfer.c mod_rlimit.c mod_auth_unix.c mod_auth.c mod_ls.c mod_log.c mod_site.c mod_delay.c mod_facts.c mod_sql.c mod_sql_postgres.c mod_sql_passwd.c mod_auth_pam.c mod_cap.c
***********************
My proftpd.conf looks like this:
# This is a basic ProFTPD configuration file (rename it to # 'proftpd.conf' for actual use. It establishes a single server # and a single anonymous login. It assumes that you have a user/group # "nobody" and "ftp" for normal operation and anon.
ServerName "ProFTPD 4 Galaxy" ServerType standalone DefaultServer on AuthPAM off SyslogFacility DAEMON SyslogLevel debug # Set up mod_sql_password - Galaxy passwords are stored as hex-encoded SHA1 SQLPasswordEngine on SQLPasswordEncoding hex AuthOrder mod_sql.c RequireValidShell off
# Set up mod_sql to authenticate against the Galaxy database SQLEngine on SQLBackend postgres SQLConnectInfo galaxy_prod@localhost:5432 galaxy password #SQLAuthTypes SHA1 SQLAuthTypes SHA1 SHA256 pbkdf2 SQLPasswordPBKDF2 SHA256 1000 24 SQLAuthenticate users SQLDefaultHomedir /var/opt/local/proftpd SQLUserInfo custom:/LookupGalaxyUser SQLPasswordUserSalt sql:/GetUserSalt #SQLNamedQuery LookupGalaxyUser SELECT "email,password,'497','495','/home/galaxy/galaxy_dist/database/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U'" SQLNamedQuery LookupGalaxyUser SELECT "email, (CASE WHEN substring(password from 1 for 6) = 'PBDKF2' THEN substring(password from 38 for 69) ELSE password END) AS password2,'galaxy','galaxy','/home/galaxy/galaxy-dist/database/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U'" SQLNamedQuery GetUserSalt SELECT "(CASE WHEN SUBSTRING (password from 1 for 6) = 'PBDKF2' THEN SUBSTRING (password from 21 for 36) END) AS salt FROM galaxy_user WHERE email='%U'"
SQLLogFile /var/log/proftpd.log SQLDefaultGID 1002 SQLDefaultUID 1002
# Port 21 is the standard FTP port. Port 21 PassivePorts 30000 40000
# Don't use IPv6 support by default. UseIPv6 off
# Umask 022 is a good standard umask to prevent new dirs and files # from being group and world writable. Umask 077
# To prevent DoS attacks, set the maximum number of child processes # to 30. If you need to allow more than 30 concurrent connections # at once, simply increase this value. Note that this ONLY works # in standalone mode, in inetd mode you should use an inetd server # that allows you to limit maximum number of processes per service # (such as xinetd). MaxInstances 30
# Set the user and group under which the server will run. User galaxy Group galaxy
# To cause every FTP user to be "jailed" (chrooted) into their home # directory, uncomment this line. DefaultRoot ~ CreateHome on dirmode 700
# Normally, we want files to be overwriteable. AllowOverwrite on AllowStoreRestart on
# Bar use of SITE CHMOD by default <Limit SITE_CHMOD> DenyAll </Limit>
# Bar use of RETR (download) since this is not a public file drop <Limit RETR> DenyAll </Limit>
*************************************************
I have found the SQLNamedQuery directives by googling around and I have figured out they should work both with old and new password encryption methods used by Galaxy. My installation however is fresh and thus I should have only password encrypted with the new method.
When I try to ftp the server this is what shows up in the log:
2013-07-20 16:35:54,618 mod_sql/4.3[4127]: >>> sql_sess_init 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: entering postgres cmd_defineconnection 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: name: 'default' 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: user: 'galaxy' 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: host: 'localhost' 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: db: 'galaxy_prod' 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: port: '5432' 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: ttl: '0' 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: exiting postgres cmd_defineconnection 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: connection 'default' successfully established 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: mod_sql engine : on 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: negative_cache : off 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: authenticate : users 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: usertable : users 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: userid field : userid 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: password field : passwd 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: UID field : uid 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: GID field : gid 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: homedir field : homedir 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: homedir(default) : '/var/opt/local/proftpd' 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: shell field : shell 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: SQLMinUserUID : 999 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: SQLMinUserGID : 999 2013-07-20 16:35:54,618 mod_sql/4.3[4127]: <<< sql_sess_init 2013-07-20 16:36:01,533 mod_sql/4.3[4127]: >>> sql_escapestr 2013-07-20 16:36:01,533 mod_sql/4.3[4127]: entering postgres cmd_escapestring 2013-07-20 16:36:01,533 mod_sql/4.3[4127]: entering postgres cmd_open 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: Postgres server version: 9.2.4 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: connection 'default' opened 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: connection 'default' count is now 2 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: exiting postgres cmd_open 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: entering postgres cmd_close 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: connection 'default' count is now 1 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: exiting postgres cmd_close 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: exiting postgres cmd_escapestring 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: <<< sql_escapestr 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: >>> sql_lookup 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: >>> process_named_query 'GetUserSalt' 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: entering postgres cmd_escapestring 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: entering postgres cmd_open 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: connection 'default' count is now 2 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: exiting postgres cmd_open 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: entering postgres cmd_close 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: connection 'default' count is now 1 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: exiting postgres cmd_close 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: exiting postgres cmd_escapestring 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: entering postgres cmd_select 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: entering postgres cmd_open 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: connection 'default' count is now 2 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: exiting postgres cmd_open 2013-07-20 16:36:01,537 mod_sql/4.3[4127]: query "SELECT (CASE WHEN SUBSTRING (password from 1 for 6) = 'PBDKF2' THEN SUBSTRING (password from 21 for 36) END) AS salt FROM galaxy_user WHERE email='federico.zambelli@gmail.com'" 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: entering postgres cmd_close 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: connection 'default' count is now 1 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: exiting postgres cmd_close 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: exiting postgres cmd_select 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: <<< process_named_query 'GetUserSalt' 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: <<< sql_lookup 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: >>> sql_pre_pass 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: <<< sql_pre_pass 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: >>> cmd_getpwnam 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: entering postgres cmd_escapestring 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: entering postgres cmd_open 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: connection 'default' count is now 2 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: exiting postgres cmd_open 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: entering postgres cmd_close 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: connection 'default' count is now 1 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: exiting postgres cmd_close 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: exiting postgres cmd_escapestring 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: cache miss for user 'federico.zambelli@gmail.com' 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: >>> sql_lookup 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: >>> process_named_query 'LookupGalaxyUser' 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: entering postgres cmd_escapestring 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: entering postgres cmd_open 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: connection 'default' count is now 2 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: exiting postgres cmd_open 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: entering postgres cmd_close 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: connection 'default' count is now 1 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: exiting postgres cmd_close 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: exiting postgres cmd_escapestring 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: entering postgres cmd_escapestring 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: entering postgres cmd_open 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: connection 'default' count is now 2 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: exiting postgres cmd_open 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: entering postgres cmd_close 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: connection 'default' count is now 1 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: exiting postgres cmd_close 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: exiting postgres cmd_escapestring 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: entering postgres cmd_select 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: entering postgres cmd_open 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: connection 'default' count is now 2 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: exiting postgres cmd_open 2013-07-20 16:36:01,540 mod_sql/4.3[4127]: query "SELECT email, (CASE WHEN substring(password from 1 for 6) = 'PBDKF2' THEN substring(password from 38 for 69) ELSE password END) AS password2,'galaxy','galaxy','/home/galaxy/galaxy-dist/database/ftp/federico.zambelli@gmail.com','/bin/bash' FROM galaxy_user WHERE email='federico.zambelli@gmail.com'" 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: entering postgres cmd_close 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: connection 'default' count is now 1 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: exiting postgres cmd_close 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: exiting postgres cmd_select 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: <<< process_named_query 'LookupGalaxyUser' 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: <<< sql_lookup 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: custom SQLUserInfo query 'LookupGalaxyUser' returned 6 columns for user 'federico.zambelli@gmail.com' 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: user UID 0 below SQLMinUserUID 999, using SQLDefaultUID 1002 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: user GID 0 below SQLMinUserGID 999, using SQLDefaultGID 1002 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: cache miss for user 'federico.zambelli@gmail.com' 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: user 'federico.zambelli@gmail.com' cached 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: + pwd.pw_name : federico.zambelli@gmail.com 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: + pwd.pw_uid : 1002 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: + pwd.pw_gid : 1002 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: + pwd.pw_dir : /home/galaxy/galaxy-dist/database/ftp/federico.zambelli@gmail.com 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: + pwd.pw_shell : /bin/bash 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: <<< cmd_getpwnam 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: >>> cmd_auth 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: entering postgres cmd_escapestring 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: entering postgres cmd_open 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: connection 'default' count is now 2 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: exiting postgres cmd_open 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: entering postgres cmd_close 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: connection 'default' count is now 1 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: exiting postgres cmd_close 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: exiting postgres cmd_escapestring 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: cache hit for user 'federico.zambelli@gmail.com' 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: >>> cmd_check 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: checking password using SQLAuthType 'sha1' 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: 'sha1' SQLAuthType handler reports failure 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: checking password using SQLAuthType 'sha256' 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: 'sha256' SQLAuthType handler reports failure 2013-07-20 16:36:01,541 mod_sql/4.3[4127]: checking password using SQLAuthType 'pbkdf2' 2013-07-20 16:36:01,547 mod_sql/4.3[4127]: 'pbkdf2' SQLAuthType handler reports failure 2013-07-20 16:36:01,547 mod_sql/4.3[4127]: <<< cmd_check 2013-07-20 16:36:01,547 mod_sql/4.3[4127]: <<< cmd_auth 2013-07-20 16:36:02,861 mod_sql/4.3[4127]: entering postgres cmd_exit
*********************************************************************
It looks like it is able to retrieve the user from the db but then it somewhat fails to check the password validity.
Thanks again.
Bye and have a nice w.e.