failed to FTP file to galaxy

Question: failed to FTP file to galaxy

5 months ago by

yuqing.hou • 0 wrote:

Hi, I can't upload file using FTP. I can not log in to the FTP server at ftp://usegalaxy.org either. I followed the link: https://galaxyproject.org/ftp-upload/ using filezilla in windows 10. Below is what filezilla tells me:

Status: Disconnected from server
Status: Resolving address of usegalaxy.org
Status: Connecting to 129.114.60.56:21...
Status: Connection established, waiting for welcome message...
Status: Initializing TLS...
Status: Verifying certificate...
Status: TLS connection established.
Status: Logged in
Status: Retrieving directory listing...
Command:    PWD
Response:   257 "/" is the current directory
Command:    TYPE I
Response:   200 Type set to I
Command:    PASV
Response:   227 Entering Passive Mode (129,114,60,56,117,160).
Command:    MLSD
Error:  The data connection could not be established: ECONNREFUSED - Connection refused by server

upload ftp galaxy • 417 views

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modified 5 months ago • written 5 months ago by yuqing.hou • 0

5 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Please see these prior post for Q&A solutions:

There are many more posts. Search with the keyword "MLSD" in the right sidebar for more where different troubleshooting cases are covered in the discussion.

Thanks! Jen, Galaxy team

ADD COMMENT • link written 5 months ago by Jennifer Hillman Jackson ♦ 25k

5 months ago by

yuqing.hou • 0

yuqing.hou • 0 wrote:

Hi Jen,

Thank you for your quick response. I read the above prior posts and tried all the things mentioned in these posts. Still can not connect to your server.

Could you check to see if there is anything that can be improved at your end? Otherwise, is there any alternative way to upload big files?

Thank you again.

ADD COMMENT • link written 5 months ago by yuqing.hou • 0

Did you try this method https://galaxyproject.org/ftp-upload/#upload-with-lftp-command-line?

You can also set up a site-specific server to usegalaxy.org within Filezilla. That is a bit more complicated but covered in the video at the same FAQ above.

If you still have trouble after that, then there could be a firewall problem. Check with your local admins, they might need to tune which sites they block. If they need help/context, have them report the problem at Gitter and ask for a how-to (ports and other technical details). This usually takes some back-n-forth to resolve so a real-time chat with the developers is faster/better. https://gitter.im/galaxyproject/Lobby

I should note that when this is reported, it is almost always from people using Filezilla on Windows. One or more settings is not correct and gets fixed (can vary) and/or setting up a site instead of using all defaults tends to resolve the problem. So, the line-command method, setting up a site in Filezilla, or test out a different FTP client are all worth a try, before checking for firewall issues with your admins. If line-command fails, then you know the issue is with a firewall.

ADD REPLY • link written 5 months ago by Jennifer Hillman Jackson ♦ 25k

5 months ago by

yuqing.hou • 0

yuqing.hou • 0 wrote:

Thank you for your quick response.

I contacted our institution's IT department. They checked the firewall and saw nothing was blocked.

I tried the command-line option and still can not connect. The whole session is copied and pasted below. The last four sentences tell the reason. Since I am new to this field, would you please help me figure out the specific reason that I failed?

Thank you.

Microsoft Windows [Version 10.0.15063]
(c) 2017 Microsoft Corporation. All rights reserved.
C:\Users\houy>ftp usegalaxy.org
Connected to usegalaxy.org.
220-usegalaxy.org FTP
This FTP server allows users to upload large data to the Galaxy server at:
https://usegalaxy.org/
 Your login uses the same credentials as your Galaxy login - email address and
 password.

 Once files are successfully uploaded, the list of files available for importing
 in to a history will be displayed in the regular Upload tool.  For assistance,
 please contact:

   galaxy-bugs@galaxyproject.org

 Files uploaded via FTP and not imported to a history within three days will be
 deleted.
220 ProFTPD 1.3.5e Server usegalaxy.org FTP (Explicit SSL/TLS on port 21)) [::ffff:129.114.60.56]
550 SSL/TLS required on the control channel
User usegalaxy.org:(none)): admin edit: full email redacted for privacy
550 SSL/TLS required on the control channel
Login failed.

ADD COMMENT • link written 5 months ago by yuqing.hou • 0

Usegalaxy.org has FTPS enabled. That means you'll need to use one of these two commands to connect line-command. Please give it a try instead, it looks like you are just using ftp with no user (-u) specified.

For explicit FTPS:

$ lftp -u user@email.edu usegalaxy.org

For implicit FTPS:

$ lftp -u user@email.edu ftps://usegalaxy.org

FAQ: https://galaxyproject.org/ftp-upload/#upload-with-lftp-command-line

ADD REPLY • link modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson ♦ 25k

5 months ago by

yuqing.hou • 0

yuqing.hou • 0 wrote:

For reference, I am on a PC, not Mac/Unix.The provided commands appeared to be for Mac.

Also, the server asked for user once it established a connection. After I entered the username and pressed return, I got the failure message. It even didn't ask for password.

I have tried Filezilla and WINSCP. Both return an error from the server, for example: WINSCP says "access denied".

I also tried to log onto fttp://usefalaxy.org using google chrome, but got no response from the website.

I am certain for all the cases the correct account name and password have been supplied.

Is it possible that my account doesn't have the permission to use ftp? Or for some reason, your server is rejecting clients?

Please advise.

ADD COMMENT • link written 5 months ago by yuqing.hou • 0

5 months ago by

Martin Čech ♦♦ 4.9k

United States

Martin Čech ♦♦ 4.9k wrote:

How large are the files you are trying to upload? With the changes in the latest Galaxy release 18.05 you should be able to upload many gigabytes directly at https://usegalaxy.org using your browser. That might save you the headache of troubleshooting something we are not able to reproduce.

ADD COMMENT • link written 5 months ago by Martin Čech ♦♦ 4.9k

5 months ago by

yuqing.hou • 0

yuqing.hou • 0 wrote:

My files are around 5 GB.

ADD COMMENT • link written 5 months ago by yuqing.hou • 0

That should work with Upload now. Please give it a try. How long the Upload takes will depend on the speed of your internet connection. We think that you shouldn't switch histories while this is going on, so plan it so that won't be a problem.

The alternative is to uninstall/reinstall Filezilla and use all of the defaults (don't change any settings). FTP is a distinct process and can run in the background without impacting the Galaxy GUI. Be sure to watch the load and reconnect, resume, then reaccept the security certificate as needed. Slower upload connection speeds can lead to broken connections. This is just how FTP works, it is not a Galaxy issue.

Hope one of these works out for you!

ADD REPLY • link written 5 months ago by Jennifer Hillman Jackson ♦ 25k

We think that you shouldn't switch histories while this is going on, so plan it so that won't be a problem.

Open a new tab with Galaxy and work there, leaving the large upload in its own tab that you don't use until finished.

ADD REPLY • link written 5 months ago by Martin Čech ♦♦ 4.9k

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