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Galaxy Administrators Course

Allow users to upload data via FTP - Exercise.

Author: Nate Coraor (2017), Abdulrahman Azab (2018)

Introduction

Loading large data into Galaxy can be difficult, especially since browser uploads do not easily support resuming transfers. You can use the venerable FTP (or preferably its secured counterpart, FTPS, or even SFTP) to allow users to upload data via an FTP client with more robust file transfer features.

Section 1 - Install ProFTPD

ProFTPD needs to be able to resolve the hostname of your VM to an IP address, you can verify that with:

$ getent hosts $(hostname)

If the output of this command if empty, then you need to add your hostname (which can be found using the hostname command) to the end of the line which starts with 127.0.0.1 in the /etc/hosts file, e.g.:

127.0.0.1 localhost <my_hostname>

For this example, we'll use ProFTPD. It's highly configurable and has a few important features we rely on, such as the ability to query users from a database, and PBKDF2 password support.

Use the system package manager to install ProFTPD together with proftpd-mod-pgsql to additionally provide PostgreSQL support:

$ sudo apt-get install proftpd-basic proftpd-mod-pgsql
Reading package lists... Done
Building dependency tree
Reading state information... Done
proftpd-basic is already the newest version (1.3.5a-1build1).
The following NEW packages will be installed:
  proftpd-mod-pgsql
0 to upgrade, 1 to newly install, 0 to remove and 61 not to upgrade.
Need to get 12.6 kB of archives.
After this operation, 503 kB of additional disk space will be used.
Do you want to continue? [Y/n]
Get:1 http://au.archive.ubuntu.com/ubuntu xenial/universe amd64 proftpd-mod-pgsql amd64 1.3.5a-1build1 [12.6 kB]
Fetched 12.6 kB in 0s (34.1 kB/s)
Selecting previously unselected package proftpd-mod-pgsql.
(Reading database ... 89076 files and directories currently installed.)
Preparing to unpack .../proftpd-mod-pgsql_1.3.5a-1build1_amd64.deb ...
Unpacking proftpd-mod-pgsql (1.3.5a-1build1) ...
Setting up proftpd-mod-pgsql (1.3.5a-1build1) ...

Section 2 - Configure ProFTPD

First, we need to instruct ProFTPD to load the mod_sql (SQL), mod_sql_postgres (PostgreSQL), and mod_sql_passwd (password hashing algorithms) modules. ProFTPD's config files can be found in /etc/proftpd and modules are loaded in modules.conf

$ cd /etc/proftpd/
$ sudo -e modules.conf

Locate the lines for the modules we need and uncomment them:

LoadModule mod_sql.c
LoadModule mod_sql_postgres.c
LoadModule mod_sql_passwd.c

Then, save and quit your editor.

Next, get your Galaxy user's UID and GID. You'll need this for the next config file:

$ id galaxy
uid=999(galaxy) gid=999(galaxy) groups=999(galaxy)

The main configuration file, proftpd.conf, will automatically include files matching /etc/proftpd/conf.d/*.conf. However, there are two options in the main configuration file we need to modify. Edit it:

$ sudo -e proftpd.conf

Comment out the User and Group options. We'll set these to the Galaxy user and group later:

#User                           proftpd
#Group                          nogroup

Create a new config at conf.d/galaxy.conf:

$ sudo -e conf.d/galaxy.conf

And add the following contents:

# Basics, some site-specific
Umask                           077

# This User & Group should be set to the actual user and group name which matches the UID & GID you will specify later in the SQLNamedQuery.
User                            galaxy
Group                           galaxy

# Cause every FTP user to be "jailed" (chrooted) into their home directory
DefaultRoot                     ~

# Automatically create home directory if it doesn't exist
CreateHome                      on dirmode 700

# Allow users to overwrite their files
AllowOverwrite                  on

# Allow users to resume interrupted uploads
AllowStoreRestart               on

# Bar use of SITE CHMOD
<Limit SITE_CHMOD>
    DenyAll
</Limit>

# Bar use of RETR (download) since this is not a public file drop
<Limit RETR>
    DenyAll
</Limit>

# Do not authenticate against real (system) users
<IfModule mod_auth_pam.c>
AuthPAM                         off
</IfModule>

# Common SQL authentication options
SQLEngine                       on
SQLPasswordEngine               on
SQLBackend                      postgres
SQLConnectInfo                  galaxy@/var/run/postgresql
SQLAuthenticate                 users

# Configuration that handles PBKDF2 encryption
# Set up mod_sql to authenticate against the Galaxy database
SQLAuthTypes                    PBKDF2
SQLPasswordPBKDF2               SHA256 10000 24
SQLPasswordEncoding             base64

# For PBKDF2 authentication
# See http://dev.list.galaxyproject.org/ProFTPD-integration-with-Galaxy-td4660295.html
SQLPasswordUserSalt             sql:/GetUserSalt

# Define a custom query for lookup that returns a passwd-like entry. Replace '999' with the UID and GID of the user running the Galaxy server
SQLUserInfo                     custom:/LookupGalaxyUser
SQLNamedQuery                   LookupGalaxyUser SELECT "email, (CASE WHEN substring(password from 1 for 6) = 'PBKDF2' THEN substring(password from 38 for 69) ELSE password END) AS password2,999,999,'/srv/galaxy/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U'"

# Define custom query to fetch the password salt
SQLNamedQuery                   GetUserSalt SELECT "(CASE WHEN SUBSTRING (password from 1 for 6) = 'PBKDF2' THEN SUBSTRING (password from 21 for 16) END) AS salt FROM galaxy_user WHERE email='%U'"

If your UID and GID were not 999, be sure to update the SQLNamedQuery LookupGalaxyUser accordingly. Thne, save and quit your editor.

Finally, restart ProFTPD:

$ sudo systemctl restart proftpd
$ systemctl status proftpd
● proftpd.service - LSB: Starts ProFTPD daemon
   Loaded: loaded (/etc/init.d/proftpd; bad; vendor preset: enabled)
   Active: active (running) since Wed 2017-02-01 04:34:42 UTC; 11s ago

Section 3 - Configure Galaxy

We need to set a few Galaxy config options. First, the diretory where files will by uploaded to (we set it in the ProFTPD config as /srv/galaxy/ftp). Second is the address that users connect to - this is only used for display purposes in the Galaxy UI:

$ sudo -u galaxy -e /srv/galaxy/config/galaxy.ini

Locate and set ftp_* accordingly:

ftp_upload_dir = /srv/galaxy/ftp
ftp_upload_site = galaxy.example.org

Then, save and quit your editor, and restart Galaxy with CTRL+C followed by sudo -Hu galaxy galaxy or sudo -Hu galaxy galaxy --stop-daemon && sudo -Hu galaxy galaxy --daemon

Section 4 - Test FTP

First of all you create an FTP directory for each Galaxy user that will use FTP

sudo -u galaxy mkdir /srv/galaxy/ftp/<galaxy-user-email>

If you have an FTP client on your system you can try it out now. Your username is the email address you registered in Galaxy with. If you don't, you can use the command line ftp client on your training instance. You can find a sample BED format file at /srv/galaxy/server/test-data/1.bed

$ ftp localhost
Connected to localhost.
220 ProFTPD 1.3.5a Server (Debian) [::1]
Name (localhost:ubuntu): [email protected]
331 Password required for [email protected]
Password:
230 User [email protected] logged in
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> lcd /srv/galaxy/server/test-data
Local directory now /srv/galaxy/server/test-data
ftp> put 1.bed
local: 1.bed remote: 1.bed
200 EPRT command successful
150 Opening BINARY mode data connection for 1.bed
226 Transfer complete
4202 bytes sent in 0.00 secs (48.2812 MB/s)
ftp> quit
221 Goodbye.

Now, in the Galaxy UI:

  1. login with the same user (if you are not already)
  2. click the upload button at the top of the tool panel
  3. click the "Choose FTP file" button
  4. you should see, and be able to choose, the file you uploaded from the dialog that opens. Once selected, clicking "Start" adds the file to your history.

Further reading