Re: [galaxy-dev] Question using sftp to upload file to galaxy

28 Jan 2019

      Hey Folks,

I tried a few times with different configurations, but none worked. Did
anyone have the successful experience that could share? :-)

Cheers,
Rui

On Sat, Jan 19, 2019 at 1:43 PM Rui Wang <ruiwang.sz@gmail.com> wrote:
...
Hey Folks,
I'm looking at the instructions of using ftp with proftpd. There is a
section talking about extending it to use sftp. However, the sample config
isn't comprehensive. I'm wondering if anyone has a working config for
reference?
What's the setting of user and group? It says it should match the one in
the SQLNamedQuery, what does it mean exactly? I start proftpd as root, but
start galaxy as bioinfoadmin(normal user with sudo).
Just fyi, my proftpd config module and config file are pasted below. I'm
working it out on a trial and error fashion, please feel free to point out
if anything is wrong!
Cheers,
Rui
modules:
$ sbin/proftpd -l
Compiled-in modules:
  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_sftp.c
  mod_cap.c
etc/proftpd.conf
ServerType                    standalone
  # You must put this in a virtual host if you want it to listen on its
own port. VHost != Apache Vhost.
  <VirtualHost 10.3.17.42>
    Port 2222
    SFTPEngine on
    AuthOrder mod_auth_unix.c mod_sql.c # If you don't do this you will
get weird disconnects
    SFTPHostKey /etc/ssh/ssh_host_rsa_key
    RequireValidShell no
    MaxLoginAttempts 6
    ServerName                      "Galaxy SFTP"
    DefaultServer                       on
    Umask                           077
    User                             bioinfoadmin
    Group                           bioinfoadmin
    UseFtpUsers off
    DefaultRoot                     ~
    AllowOverwrite                  on
    AllowStoreRestart               on
    SQLEngine                       on
    SQLGroupInfo                    sftp_groups name id members
# Do not authenticate against real (system) users
<IfModule mod_auth_pam.c>
AuthPAM                         off
</IfModule>
# Common SQL authentication options
SQLPasswordEngine               on
SQLBackend                      postgres
SQLConnectInfo                  galaxy@galaxy.my.org:5432 bioinfoadmin
dbpwd
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
SQLPasswordUserSalt             sql:/GetUserSalt
# Define a custom query for lookup that returns a passwd-like entry.
Replace 512s 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
password2,512,512,'/media/galaxy/galaxy/database/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'"
  </VirtualHost>
# Don't use IPv6 support by default.
UseIPv6                         off
MaxInstances                    30
# To cause every FTP user to be "jailed" (chrooted) into their home
# directory, uncomment this line.
# 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>
~