- You want to enable FTP file uploads?
- You are happy and able to use ProFTPd?
- You want to authenticate off Active Directory?
- You want Galaxy to actually find the uploaded files?
Yes, Yes, Yes and Of_Course? Read on..
Galaxy grew up serving the entire internet and cannot assume a username is unique so it uses email-addresses as its user-names.
Once an "ftp_upload_dir" is configured, it assumes that any uploaded files are to be found in the directory \<ftp_upload_dir>/
If it's empty or not there Galaxy reports, "Your FTP upload directory contains no files."
Galaxy checks every time you click Get Data : Upload File
Galaxy exchanges no messages directly with the FTP server, if files are there, it shows them no matter how they got there.
Your Galaxy serves a single institution with an AD domain and you're already using it to authenticate users in the Galaxy web pages.
config/galaxy.ini file probably has lines like this in the section
# Enable Galaxy's "Upload via FTP" interface.:
use_remote_user = True remote_user_maildomain = example.domain ftp_upload_dir = /galaxy/database/ftp
Line 1 means you are already using remote (apache or nginx) authentication and that your users log in using their ident as their name not their email.
Line 2 means Galaxy is appending a fixed string "@example.domain" to ALL users to convert from ident to email.
Line 3 tells Galaxy to look in "/galaxy/database/ftp/
Getting a version of ProFTPd that will actually do what it says it will
For this recipe to work will need at least these versions
- proftpd version 1.3.4
- proftpd-mod-ldap version 2.9.2 NOTE: Ubuntu-12.10 apt-get gives you version 2.9.0 which WILL NOT WORK!
The functionality of defining where home dir is and creating it has just been moved from mod_ldap into proftpd itself.
The extra functionality specifying it using a string containing %u is new to the internal proftpd.
Using the versions specified and re-specifying the %u string to both proftpd and mod-ldap makes it not just accept the string but actually create the directory if it doesn't already exist.
# This tells proftpd to create it if necessary and chroot to it DefaultRoot "/email@example.com" CreateHome on 700 # This tells mod_ldap the same thing LDAPGenerateHomedir on 700 LDAPGenerateHomedirPrefix "/firstname.lastname@example.org" LDAPForceGeneratedHomedir on LDAPGenerateHomedirPrefixNoUsername on
Here is a commented more complete file from /etc/proftpd/proftpd.conf
# Load LDAP module LoadModule mod_ldap.c # Include some other modules Include /etc/proftpd/modules.conf # Users require a valid shell listed in /etc/shells to login. # Use this directive to release that constrain. RequireValidShell off # Set the user and group that the server normally runs at. User galaxy Group galaxy # Umask 022 is a good standard umask to prevent new files and dirs # (second parm) from being group and world writable. Umask 137 027 # Normally, we want files to be overwriteable. AllowOverwrite on # Uncomment this if you are using NIS or LDAP via NSS to retrieve passwords: # PersistentPasswd off # Galaxy users are not necessarily SSH users, so don't authenticate against real (system) users AuthPAM off # All authentication is via LDAP to AD #AuthOrder mod_auth_pam.c* mod_auth_unix.c AuthOrder mod_ldap.c # You MUST NOT use URL style LDAPServer LDAPServer ad-server.example.domain:389 # I can't get this to work, need to fiddle with certificates more #LDAPUseTLS on # You can map fields using LDAPAttr # LDAPAttr expectedField "weird AD name with spaces and all sorts of crap" LDAPAttr homeDirectory "unixHomeDirectory" # LDAPBindDN "CN=<read-only-account>,OU=Special Accounts,DC=ad,DC=example,DC=domain" "password" # This defines the scope and search filter to find a user in AD LDAPUsers "OU=People,DC=ad,DC=example,DC=domain" "(cn=%u)" # With this LDAP re-binds to AD as the user using the password supplied # If it works, you're in! LDAPAuthBinds on LDAPDefaultUID "<uid-number-galaxy-is-running-as>" LDAPDefaultGID "<gid-number-galaxy-is-running-as>" # Force those numbers even if LDAP finds a valid UID/GID LDAPForceDefaultUID on LDAPForceDefaultGID on LDAPGenerateHomedir on 700 LDAPGenerateHomedirPrefix "/email@example.com" # Force this homedir even if LDAP said something different LDAPForceGeneratedHomedir on # The username is already incorporated in the %u, use this or it will get appended again LDAPGenerateHomedirPrefixNoUsername on TransferLog /var/log/proftpd/xferlog SystemLog /var/log/proftpd/proftpd.log # You need this or users will get their passwords exposed across the network in the clear Include /etc/proftpd/tls.conf # These "virtuals" allow more than 1 proftpd # to run on the same host using different IPs. #Include /etc/proftpd/virtuals.conf # Cause every FTP user to be "jailed" (chrooted) into their home directory DefaultRoot "/firstname.lastname@example.org" # Automatically create home directory if it doesn't exist CreateHome on 700 # Allow users to overwrite their files AllowOverwrite on # Allow users to resume interrupted uploads AllowStoreRestart on
Where ever it's getting the information mod_ldap is looking for:
Configuring ProFTPD with OpenLDAP
Helena Rasche found a set of working options for using ProFTPD with OpenLDAP servers (instead of AD).
This configuration file can be modified and placed in
Using the /conf.d/ directory, you can allow the ProFTPd to serve both local users (with PAM authentication) in the main configuration file, AND galaxy users on another port.
<VirtualHost xxx.yyy.zzz> RequireValidShell off User galaxy Group galaxy Umask 137 027 AllowOverwrite on # Ensure auth is LDAP AuthPAM off AuthOrder mod_ldap.c # Serve this VirtualHost on port 4000 Port 4000 # LDAP Bind information LDAPServer ldaps://xxx.yyy.zzz/??sub LDAPUsers "ou=People,dc=yyy,dc=zzz" "(uid=%u)" LDAPAuthBinds on # Force those numbers even if LDAP finds a valid UID/GID LDAPDefaultUID 1003 LDAPDefaultGID 1003 LDAPForceDefaultUID on LDAPForceDefaultGID on # Please generate home dir with user/group rwx permissions. Could probably be stricter CreateHome on 770 LDAPGenerateHomedir on 770 # Force this homedir even if LDAP said something different LDAPForceGeneratedHomedir on LDAPGenerateHomedirPrefix "/email@example.com" # The username is already incorporated in the %u, use this or it will get appended again LDAPGenerateHomedirPrefixNoUsername on TransferLog /var/log/proftpd/xfer-galaxy.log # Cause every FTP user to be "jailed" (chrooted) into their home directory DefaultRoot "/firstname.lastname@example.org" # Allow users to resume interrupted uploads AllowStoreRestart on # I set these as my passive ports because I run a very strict firewall. Change as needed PassivePorts 49152 50000 </VirtualHost>
Notably, this configuration allows a galaxy virtualhost to coexist with the normal FTP capabilities provided by ProFTPd, so users can still access their home directories AND galaxy users can upload to galaxy. Authentication can of course be changed to suit one's needs.
If you're running the galaxy FTP portion under a VirtualHost, like described above, you'll notice that TLS directives placed in the main proftpd.conf file do not apply to VirtualHosts. As such, you can add a section that looks like this to every VirtualHost that needs to be secured
<IfModule mod_tls.c> TLSEngine on TLSLog /var/log/proftpd/tls.galaxy.log # Your cert and private key TLSRSACertificateFile /etc/ssl/certs/my.crt TLSRSACertificateKeyFile /etc/ssl/private/my.key TLSCACertificateFile /etc/ssl/certs/ca.bundle # I've found that this is required for FileZilla TLSOptions NoCertRequest EnableDiags NoSessionReuseRequired # Most clients won't be sending certs TLSVerifyClient off TLSRequired on </IfModule>