Question: ftp upload galaxy local
2
gravatar for bc335
3.6 years ago by
bc33520
United States
bc33520 wrote:

Hi,

I installed Galaxy locally on my laptop (working on ubuntu 14.04) following these instructions: https://wiki.galaxyproject.org/Admin/GetGalaxy and all went well. I was even able to add new modules.

I tried also to configure the galaxy for ftp file transfer but the instructions on the website are not clear https://wiki.galaxyproject.org/Admin/Config/UploadviaFTP. especially the parts: Configuring the database server and after. There is no indication on the files to modify and how to do it.

I am using a Filezilla for file transfert and it's working fine for the Galaxy main server.

Can anyone help me?

Thanks.

 

db ftp galaxy local • 1.4k views
ADD COMMENTlink modified 3.6 years ago by Martin Čech ♦♦ 4.6k • written 3.6 years ago by bc33520
0
gravatar for Martin Čech
3.6 years ago by
Martin Čech ♦♦ 4.6k
United States
Martin Čech ♦♦ 4.6k wrote:

You need to install FTP server software and configure it in a way, that it can read from Galaxy's database (to authenticate users with the same credentials). I made the wiki page a little clearer. Let me know if you have more questions.

ADD COMMENTlink written 3.6 years ago by Martin Čech ♦♦ 4.6k

Hi, I have a similar question and don't want to start a new thread because of it. ( I only assume you are the same Martin Cech who is administering the galaxy page.) Regarding the ./configure in the instructions on https://wiki.galaxyproject.org/Admin/Config/UploadviaFTP what does it refer to? galaxy-dist does not carry a configure file. Could you please explain these instructions?

Thanks. 

 

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by karolpal.jr10

It is the configure script of ProFTPd. The FTP server does not come in bundle with Galaxy, you have to download, install and set up your own. We recommend ProFTPd and the page you linked provides our configuration for it.

more on configure script: http://en.wikipedia.org/wiki/Configure_script
more on proftd compilation: http://www.proftpd.org/docs/howto/Compiling.html

That said, if this is all new, you might want to ask a local with some admin experience to help you as compiling can turn non-trivial. Alternatively you can use some install-friendlier FTP server, see the list: http://en.wikipedia.org/wiki/List_of_FTP_server_software

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by Martin Čech ♦♦ 4.6k

I see, I was a little confused by different instructions but I see you're doing a good job cleaning and maintaining the the wiki. I have in fact installed ProFTPd throu a debian package so I'll try to install it manually.

Thanks for your fast and informative reply.

ADD REPLYlink written 3.6 years ago by karolpal.jr10

 

Ok,

I have one more question... I think I'm almost there. Galaxy uses postgresql with authentication. Proftpd is working. I can see my user in the database however I can't log in throu filezilla. When I search the log file of proftpd I get 

Nov 05 18:43:54 galaxy proftpd[12082] galaxy (::ffff:147.251.158.38[::ffff:147.251.158.38]): retrieved UID 65533 for user 'k....l@gmail.com'
Nov 05 18:43:54 galaxy proftpd[12082] galaxy (::ffff:147.251.158.38[::ffff:147.251.158.38]): no supplemental groups found for user 'k....l@gmail.com'
Nov 05 18:43:54 galaxy proftpd[12082] galaxy (::ffff:147.251.158.38[::ffff:147.251.158.38]): mod_sql_passwd/0.2:expected '21b76ecb6da99a174bbf00c059b77cdf', got 'PBKDF2$sha256$10000$CRGjgzvrM2VaLKZS$sRHQAJZAmyph6rs4KZVpJErJ+t13K7hU'
Nov 05 18:43:54 galaxy proftpd[12082] galaxy (::ffff:147.251.158.38[::ffff:147.251.158.38]): USER k....l@gmail.com (Login failed): No such user found

So proftpd is successfully querying the 'password' field of my galaxy_user... however the output is somehow more complex (could it be that it's changed in newer versions of galaxy?)

I set my galaxy.conf according to your instructions (although I'm not quite sure if I got the GID and PID right)

Thanks in advance..

 

The output from SQL.log:

Nov 05 20:33:21 mod_sql/4.2.5[12514]: query "SELECT email,password,'512','512','/home/galaxy/galaxy-dist/database/ftp/k....l@gmail.com','/b
in/bash' FROM galaxy_user WHERE email='k....l@gmail.com'"
Nov 05 20:33:21 mod_sql/4.2.5[12514]: entering     postgres cmd_close
Nov 05 20:33:21 mod_sql/4.2.5[12514]: connection 'default' count is now 1
Nov 05 20:33:21 mod_sql/4.2.5[12514]: exiting     postgres cmd_close
Nov 05 20:33:21 mod_sql/4.2.5[12514]: exiting     postgres cmd_select
Nov 05 20:33:21 mod_sql/4.2.5[12514]: <<< process_named_query 'LookupGalaxyUser'
Nov 05 20:33:21 mod_sql/4.2.5[12514]: <<< sql_lookup
Nov 05 20:33:21 mod_sql/4.2.5[12514]: user UID 512 below SQLMinUserUID 999, using SQLDefaultUID 65533
Nov 05 20:33:21 mod_sql/4.2.5[12514]: user GID 512 below SQLMinUserGID 999, using SQLDefaultGID 65533
Nov 05 20:33:21 mod_sql/4.2.5[12514]: cache miss for user 'k....l@gmail.com'
Nov 05 20:33:21 mod_sql/4.2.5[12514]: user 'k....l@gmail.com' cached
Nov 05 20:33:21 mod_sql/4.2.5[12514]: + pwd.pw_name  : k....l@gmail.com
Nov 05 20:33:21 mod_sql/4.2.5[12514]: + pwd.pw_uid   : 65533
Nov 05 20:33:21 mod_sql/4.2.5[12514]: + pwd.pw_gid   : 65533
Nov 05 20:33:21 mod_sql/4.2.5[12514]: + pwd.pw_dir   : /home/galaxy/galaxy-dist/database/ftp/k....l@gmail.com
Nov 05 20:33:21 mod_sql/4.2.5[12514]: + pwd.pw_shell : /bin/bash
Nov 05 20:33:21 mod_sql/4.2.5[12514]: <<< cmd_getpwnam
Nov 05 20:33:21 mod_sql/4.2.5[12514]: >>> cmd_auth
Nov 05 20:33:21 mod_sql/4.2.5[12514]: entering     postgres cmd_escapestring
Nov 05 20:33:21 mod_sql/4.2.5[12514]: entering     postgres cmd_open
Nov 05 20:33:21 mod_sql/4.2.5[12514]: connection 'default' count is now 2
Nov 05 20:33:21 mod_sql/4.2.5[12514]: exiting     postgres cmd_open
Nov 05 20:33:21 mod_sql/4.2.5[12514]: entering     postgres cmd_close
Nov 05 20:33:21 mod_sql/4.2.5[12514]: connection 'default' count is now 1
Nov 05 20:33:21 mod_sql/4.2.5[12514]: exiting     postgres cmd_close
Nov 05 20:33:21 mod_sql/4.2.5[12514]: exiting     postgres cmd_escapestring
Nov 05 20:33:21 mod_sql/4.2.5[12514]: cache hit for user 'k....l@gmail.com'
Nov 05 20:33:21 mod_sql/4.2.5[12514]: >>> cmd_check
Nov 05 20:33:21 mod_sql/4.2.5[12514]: checking password using SQLAuthType 'sha1'
Nov 05 20:33:21 mod_sql/4.2.5[12514]: 'sha1' SQLAuthType handler reports failure

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by karolpal.jr10

Hi,

By default, Galaxy uses a PBKDF2 scheme to store passwords. This can be disabled by setting `use_pbkdf2 = False` in `galaxy.ini` and restarting. Once restarted, any existing users will need to change their passwords to change the encryption scheme on their user record to SHA1.

Alternatively, you can use ProFTPD 1.3.5's new PBKDF2 support:

http://bugs.proftpd.org/show_bug.cgi?id=4052

I don't know of anyone who's tried it out so I don't have an example configuration at this point. But it was developed by the ProFTPD author to work with the way we use PBKDF2, so it should work.

ADD REPLYlink written 3.6 years ago by Nate Coraor3.1k

Thanks, works perfectly :)

ADD REPLYlink written 3.6 years ago by karolpal.jr10
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