Re: [galaxy-dev] FTP GALAXY

2011-12-08 Thread James Boocock

Hi

We have set up galaxy in a production environment and our galaxy users 
can connect to the FTP and upload files. No worries.


The settings in the universe file seem correct and are.

ftp_upload_dir = /home/galaxy/galaxy-dist/database/ftp


It creates the directory and uploads the file. But when the user signs 
into galaxy they cannot view their file in the get data  - from files 
on my computer.


Proftp config is listed below.

Cheers James Boocock

ServerName  Public Galaxy FTP
ServerType  standalone
DefaultServer   on
Port21
Umask   077
SyslogFacility  DAEMON
SyslogLevel debug
MaxInstances30
Usernobody
Group   nogroup
DisplayConnect  /etc/opt/local/proftpd_welcome.txt

# Passive port range for the firewall
PassivePorts3 4

# 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 1700

# 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

# Do not authenticate against real (system) users
AuthPAM off

# Set up mod_sql_password - Galaxy passwords are stored as hex-encoded SHA1
SQLPasswordEngine   on
SQLPasswordEncoding hex

# Set up mod_sql to authenticate against the Galaxy database
SQLEngine   on
SQLBackend  postgres
SQLConnectInfo  galaxydb galaxyftp 1234
SQLAuthTypesSHA1
SQLAuthenticate users

# An empty directory in case chroot fails
SQLDefaultHomedir   /var/opt/local/proftpd

# Define a custom query for lookup that returns a passwd-like entry.  
UID and GID should match your Galaxy user.

# Do not authenticate against real (system) users
AuthPAM off

# Set up mod_sql_password - Galaxy passwords are stored as hex-encoded SHA1
SQLPasswordEngine   on
SQLPasswordEncoding hex

# Set up mod_sql to authenticate against the Galaxy database
SQLEngine   on
SQLBackend  postgres
SQLConnectInfo  galaxydb galaxyftp 1234
SQLAuthTypesSHA1
SQLAuthenticate users

# An empty directory in case chroot fails
SQLDefaultHomedir   /var/opt/local/proftpd

# Define a custom query for lookup that returns a passwd-like entry.  
UID and GID should match your Galaxy user.

SQLUserInfo custom:/LookupGalaxyUser
SQLNamedQuery   LookupGalaxyUser SELECT 
email,password,'512','512','/home/galaxy/galaxy-dist/database/ftp/%U','/bin/bash' 
FROM galaxy_user WHERE email='%U'




SQLUserInfo custom:/LookupGalaxyUser
SQLNamedQuery   LookupGalaxyUser SELECT 
email,password,'512','512','/home/galaxy/galaxy-dist/database/ftp/%U','/bin/bash' 
FROM galaxy_user WHERE email='%U'



/Limit

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Re: [galaxy-dev] FTP GALAXY

2011-12-08 Thread Nate Coraor
On Dec 7, 2011, at 10:19 PM, James Boocock wrote:

 Hi
 
 We have set up galaxy in a production environment and our galaxy users can 
 connect to the FTP and upload files. No worries.
 
 The settings in the universe file seem correct and are.
 
 ftp_upload_dir = /home/galaxy/galaxy-dist/database/ftp
 
 
 It creates the directory and uploads the file. But when the user signs into 
 galaxy they cannot view their file in the get data  - from files on my 
 computer.

Hi James,

You also need to set ftp_upload_site, if you haven't done so.

--nate

 
 Proftp config is listed below.
 
 Cheers James Boocock
 
 ServerName  Public Galaxy FTP
 ServerType  standalone
 DefaultServer   on
 Port21
 Umask   077
 SyslogFacility  DAEMON
 SyslogLevel debug
 MaxInstances30
 Usernobody
 Group   nogroup
 DisplayConnect  /etc/opt/local/proftpd_welcome.txt
 
 # Passive port range for the firewall
 PassivePorts3 4
 
 # 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 1700
 
 # 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
 
 # Do not authenticate against real (system) users
AuthPAM off
 
 # Set up mod_sql_password - Galaxy passwords are stored as hex-encoded SHA1
SQLPasswordEngine   on
SQLPasswordEncoding hex
 
 # Set up mod_sql to authenticate against the Galaxy database
SQLEngine   on
SQLBackend  postgres
SQLConnectInfo  galaxydb galaxyftp 1234
SQLAuthTypesSHA1
SQLAuthenticate users
 
 # An empty directory in case chroot fails
SQLDefaultHomedir   /var/opt/local/proftpd
 
 # Define a custom query for lookup that returns a passwd-like entry.  UID and 
 GID should match your Galaxy user.
 # Do not authenticate against real (system) users
AuthPAM off
 
 # Set up mod_sql_password - Galaxy passwords are stored as hex-encoded SHA1
SQLPasswordEngine   on
SQLPasswordEncoding hex
 
 # Set up mod_sql to authenticate against the Galaxy database
SQLEngine   on
SQLBackend  postgres
SQLConnectInfo  galaxydb galaxyftp 1234
SQLAuthTypesSHA1
SQLAuthenticate users
 
 # An empty directory in case chroot fails
SQLDefaultHomedir   /var/opt/local/proftpd
 
 # Define a custom query for lookup that returns a passwd-like entry.  UID and 
 GID should match your Galaxy user.
SQLUserInfo custom:/LookupGalaxyUser
SQLNamedQuery   LookupGalaxyUser SELECT 
 email,password,'512','512','/home/galaxy/galaxy-dist/database/ftp/%U','/bin/bash'
  FROM galaxy_user WHERE email='%U'
 
 
 
SQLUserInfo custom:/LookupGalaxyUser
SQLNamedQuery   LookupGalaxyUser SELECT 
 email,password,'512','512','/home/galaxy/galaxy-dist/database/ftp/%U','/bin/bash'
  FROM galaxy_user WHERE email='%U'
 
 
 /Limit
 
 ___
 Please keep all replies on the list by using reply all
 in your mail client.  To manage your subscriptions to this
 and other Galaxy lists, please use the interface at:
 
 http://lists.bx.psu.edu/


___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/