tag:blogger.com,1999:blog-5290934002193555057.post1455106013054169110..comments2022-05-02T08:00:44.233+01:00Comments on Galactic Engineer: FTP upload to Galaxy using ProFTPd and PBKDF2pjbhttp://www.blogger.com/profile/02877142465318426440noreply@blogger.comBlogger14125tag:blogger.com,1999:blog-5290934002193555057.post-80143555958265803012020-04-22T10:32:26.363+01:002020-04-22T10:32:26.363+01:00Hello Luc
It's been a while since I set up pr...Hello Luc<br /><br />It's been a while since I set up proFTPD and I'm not sure I can remember all the details, however I'll try and help.<br /><br />In the configuration that we're using, proFTPD is run as a system service on the server and that requires root permissions to set up. However within the service proFTPD itself is run as user 'nobody'.<br /><br />So that suggests to me that you should in principle be able to run proFTPD manually without root privileges.<br /><br />For your specific errors the only thing I can think of if in your 'proftpd.conf' file you're specifying 'User' and/or 'Group' to be different from the (non-root) user you're trying to run proFTPD. If this is the case then maybe try removing those from the '.conf' file.<br /><br />Otherwise I'd suggest searching a bit on Google or ProFTPD forums to see if there are other suggestions.<br /><br />Good luck with resolving your issues!<br />pjbhttps://www.blogger.com/profile/02877142465318426440noreply@blogger.comtag:blogger.com,1999:blog-5290934002193555057.post-11344260635611154292020-04-20T14:56:21.178+01:002020-04-20T14:56:21.178+01:00Hi, it it mandatory to be root to run proFTPD ? I ...Hi, it it mandatory to be root to run proFTPD ? I would like to install a local instance on a cluster but without root permissions. Do i need specific activation in the conf file ?<br /><br />Thanks,<br />Luc<br />I have the following problem when i try proftpd: <br />[galaxy@node01 ~]$ proftpd --config /media/vol2/home/galaxy/proftpd.conf -t<br />Checking syntax of configuration file<br />node01 - ROOT PRIVS: unable to seteuid(): Operation not permitted<br />node01 - ROOT PRIVS: unable to setegid(): Operation not permitted<br />node01 - RELINQUISH PRIVS: unable to seteuid(PR_ROOT_UID): Operation not permitted<br />node01 - RELINQUISH PRIVS: unable to setegid(session.gid): Operation not permitted<br />node01 - RELINQUISH PRIVS: unable to seteuid(session.uid): Operation not permitted<br />node01 - RELINQUISH PRIVS: unable to seteuid(PR_ROOT_UID): Operation not permitted<br />node01 - RELINQUISH PRIVS: unable to setegid(session.gid): Operation not permitted<br />node01 - RELINQUISH PRIVS: unable to seteuid(session.uid): Operation not permitted<br />Syntax check complete.<br />node01 - RELINQUISH PRIVS: unable to seteuid(PR_ROOT_UID): Operation not permitted<br />node01 - RELINQUISH PRIVS: unable to setegid(session.gid): Operation not permitted<br />node01 - RELINQUISH PRIVS: unable to seteuid(session.uid): Operation not permittedLuchttps://www.blogger.com/profile/11891478272387762072noreply@blogger.comtag:blogger.com,1999:blog-5290934002193555057.post-73927228545722443452018-08-30T10:31:29.334+01:002018-08-30T10:31:29.334+01:00Hello hangz
I'm not sure how much help I can ...Hello hangz<br /><br />I'm not sure how much help I can give you unless you're more specific about the parts which are failing.<br /><br />However it might be that you no longer need to enable FTP upload - if you're using Galaxy release 18.05 or newer then this supports unlimited browser upload size without any configuration, which "... should effectively eliminate browser-based limitations on the size of files that can be uploaded to Galaxy".<br /><br />See https://docs.galaxyproject.org/en/release_18.05/releases/18.05_announce.html for more details.<br /><br />HTH!pjbhttps://www.blogger.com/profile/02877142465318426440noreply@blogger.comtag:blogger.com,1999:blog-5290934002193555057.post-1103389946174461662018-04-18T10:20:47.771+01:002018-04-18T10:20:47.771+01:00Hi,
I'm working on uploading big file via FTP...Hi,<br /> I'm working on uploading big file via FTP. Except that, I must go to install FTP due to my boss's request while I just an intern. I wish i could get your help, please.<br /> Here is the thing, I installed the proFTPd via the command of `yum install proftpd proftpd-postgersql`. And there is no error within the installation process.And ProFTPd version 1.3.5e.<br /> According to the documentation, i need to achieve the part of `Allow your FTP server to read Galaxy's database`. I think the reason why we take this part is that ensuring FTP could use the username and password of Galaxy user. However, I just can't understand the documentation. It's too abstract for me...<br /> Regards,<br /> hangzhangzhttps://www.blogger.com/profile/01404535889059875100noreply@blogger.comtag:blogger.com,1999:blog-5290934002193555057.post-78651347222914626162017-11-23T09:01:55.104+00:002017-11-23T09:01:55.104+00:00Hello Mohan
Sorry you're having problems sett...Hello Mohan<br /><br />Sorry you're having problems setting up a Galaxy instance. I'm not sure I can help with this specific problem however, as it sounds like a more general issue with the configuration of your server.<br /><br />You could try goggling the error message that you get from the "sudo yum install ..." command and see if anything comes up.<br /><br />Otherwise I suggest you try contacting the Galaxy developers mailing list to see if someone there can help: https://lists.galaxyproject.org/listinfo/galaxy-dev/<br /><br />Good luck!pjbhttps://www.blogger.com/profile/02877142465318426440noreply@blogger.comtag:blogger.com,1999:blog-5290934002193555057.post-65452465381295634392017-11-16T14:03:00.925+00:002017-11-16T14:03:00.925+00:00Hi,
I am new to Linux and just started to establ...Hi, <br /><br />I am new to Linux and just started to establish a local instance of galaxy.<br />When I am trying to run this command <br /><br />sudo yum install proftpd proftpd-postgresql<br /><br />I get the following error. <br /><br />There are no enabled repos.<br /> Run "yum repolist all" to see the repos you have.<br /> You can enable repos with yum-config-manager --enable <br /><br />I don't know how to setup a repo for my case.<br /><br />Kindly help<br />Thank you<br />Mohanmohanhttps://www.blogger.com/profile/13377507077572566840noreply@blogger.comtag:blogger.com,1999:blog-5290934002193555057.post-63373350659969706122015-07-14T12:56:19.427+01:002015-07-14T12:56:19.427+01:00Hello Rodrigo
Thanks for your comment and the add...Hello Rodrigo<br /><br />Thanks for your comment and the additional information.<br /><br />In fact it looks as if the values you use should be generally correct, as the hashed password part of the 'password' database field does seem to be 32 characters long (not 69 as implied by my example).<br /><br />As the value of 69 works for us, I wonder if different versions of PostgreSQL handle the 'substring' function differently - with some returning an error if it tries to get more characters than the string contains. We have version 8.4.18.<br /><br />(For anyone else interested in what's happening here, the 'password' field in the database is constructed by the 'hash_password_PBKDF2' function in .../lib/galaxy/security/passwords.py - which stores various pieces of information - separated by dollar signs - in a single string which looks like e.g.:<br /><br />PBKDF2$sha256$10000$DRQfphKq7tL/TLFa$uZ31gvmzOP2Jqy00Wbbg4o0Cb2PG/ZTr<br /><br />So ProFTPd needs to cut this string up using the Postgres 'substring' function in order to get the actual hashed password - which in this example it starts at position 38 and is 32 characters long.)<br /><br />Thanks again!pjbhttps://www.blogger.com/profile/02877142465318426440noreply@blogger.comtag:blogger.com,1999:blog-5290934002193555057.post-10266770873024621452015-07-08T23:23:35.079+01:002015-07-08T23:23:35.079+01:00Hi Peter, I need change "password from 38 for...Hi Peter, I need change "password from 38 for 69" to "password from 38 for 32" in LookupGalaxyUser. Now, it's all work! Thanks for help!<br /><br />Regards.Anonymoushttps://www.blogger.com/profile/07776290110789995063noreply@blogger.comtag:blogger.com,1999:blog-5290934002193555057.post-64381833981746000682015-06-08T14:01:07.001+01:002015-06-08T14:01:07.001+01:00Great - glad you managed to work it out.Great - glad you managed to work it out.pjbhttps://www.blogger.com/profile/02877142465318426440noreply@blogger.comtag:blogger.com,1999:blog-5290934002193555057.post-44686680253514380722015-06-08T12:55:03.274+01:002015-06-08T12:55:03.274+01:00It seems the error crept in from legacy job runner...It seems the error crept in from legacy job runner settings. The old [galaxy:tool_runners] format for setting them was being read incorrectly which caused the FTP settings to be read incorrectly as they are sequential in the galaxy.ini file.<br /><br />Anyhow, it's working now. Thanx again<br />gkniGhtfallhttps://www.blogger.com/profile/04361997458999844428noreply@blogger.comtag:blogger.com,1999:blog-5290934002193555057.post-86860611360671025062015-06-08T10:05:32.041+01:002015-06-08T10:05:32.041+01:00Hello Gordon
Thanks for your comment - the only t...Hello Gordon<br /><br />Thanks for your comment - the only thing I can think of is, did you also set the "ftp_upload_dir" and "ftp_upload_site" parameters in your Galaxy config file (i.e. galaxy.ini, or universe_wsgi.ini if using an older version of the Galaxy codebase)?<br /><br />I think if either are not set then you won't be able to access the uploaded files from Galaxy.<br /><br />Hope this helps!pjbhttps://www.blogger.com/profile/02877142465318426440noreply@blogger.comtag:blogger.com,1999:blog-5290934002193555057.post-50102887253187001002015-06-05T11:28:19.575+01:002015-06-05T11:28:19.575+01:00Hi pjb
Great post, very helpful thanx a million.
...Hi pjb<br /><br />Great post, very helpful thanx a million.<br /><br />Following this, setting everything up using ProFTPd and MySQL, everything works perfectly fine except that the FTP upload option is not presented to me in the Galaxy interface. File is tranferred to crrect directory, permissions are correct etc. I just don't have the FTP upload option...<br /><br />Any tips?<br />gordonkniGhtfallhttps://www.blogger.com/profile/04361997458999844428noreply@blogger.comtag:blogger.com,1999:blog-5290934002193555057.post-79850827628757653632015-05-28T10:16:31.223+01:002015-05-28T10:16:31.223+01:00Hello Jana
Sorry you're having problems, to t...Hello Jana<br /><br />Sorry you're having problems, to try and answer your questions:<br /><br />1. Yes, the real password should be substituted for 'dbpassword' in the examples<br /><br />2. I haven't encountered the error about "galaxy_user"' not existing before. This is a table in the Galaxy database that should be created when Galaxy is installed and run for the first time.<br /><br />Assuming you're following the instructions in the Galaxy documentation https://wiki.galaxyproject.org/Admin/Config/UploadviaFTP it suggests to me that there is a problem with the setup of the Postgres database.<br /><br />Searching around I've found this forum thread which might help:<br />http://dev.list.galaxyproject.org/Database-and-FTP-setup-tp4663433p4663434.html<br /><br />If you're still having problems then my suggestion would be to post the details of your problem and your Galaxy setup to the Galaxy developer list (see http://dev.list.galaxyproject.org/ for more details).<br /><br />Sorry not to be able to help more with this one - good luck!pjbhttps://www.blogger.com/profile/02877142465318426440noreply@blogger.comtag:blogger.com,1999:blog-5290934002193555057.post-89287437457888994072015-05-27T09:48:02.613+01:002015-05-27T09:48:02.613+01:00Hello blogger,
Thank you for this detailed proced...Hello blogger,<br /><br />Thank you for this detailed procedure on FTP based file transfer in Galaxy..<br />Since iam new to SQL/database handling, im wondering whether the term 'dbpassword' in the following sentence is a literal or it should be substituted for a real password.<br /><br />galaxydb=# ALTER ROLE galaxyftp PASSWORD 'dbpassword';<br />ALTER ROLE<br /><br />Also, iam getting an error while running the following command<br /><br />galaxydb=# GRANT SELECT ON galaxy_user TO galaxyftp; <br /><br />ERROR: relation "galaxy_user" does not exist<br /><br />I appreciate any help in sorting out this problem...<br /><br />Thank you!Anonymousnoreply@blogger.com