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documentation in the wiki about configuring proftpd is outdated since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.zambe...@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.zambe...@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.zambe...@gmail.com','/bin/bash'
FROM galaxy_user WHERE email='federico.zambe...@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.zambe...@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.zambe...@gmail.com'
2013-07-20 16:36:01,541 mod_sql/4.3[4127]: user
'federico.zambe...@gmail.com' cached
2013-07-20 16:36:01,541 mod_sql/4.3[4127]: + pwd.pw_name :
federico.zambe...@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.zambe...@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.zambe...@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.
--
============================================
Federico Zambelli, Ph.D.
Bioinformatics, Evolution and Comparative Genomics Lab
Dept. of Biosciences
University of Milano - Italy
What can be asserted without proof can be dismissed without proof.
============================================
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