From e75a4c32c18fa4e92d23caf979ddd7bf5edb99db Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Fri, 22 Nov 2024 12:06:02 +0100 Subject: [PATCH 1/5] update ftp info --- content/ftp-upload/index.md | 53 ++++++++++++++----------------------- 1 file changed, 20 insertions(+), 33 deletions(-) diff --git a/content/ftp-upload/index.md b/content/ftp-upload/index.md index cef7770dce..3a07f1a753 100644 --- a/content/ftp-upload/index.md +++ b/content/ftp-upload/index.md @@ -2,17 +2,17 @@ title: Galaxy FTP Upload --- - - # File Upload via FTP Uploading data directly from the browser can be unreliable and cumbersome. -Because of this some Galaxies including the [Main](/main/) allow you to upload data via FTP. +Because of this some Galaxy instances allow you to upload data via FTP. FTP will allow you to monitor the upload status as well as resume interrupted transfers. Compression types .gz/.gzip, .bz/.bzip, .bz2/.bzip2, and single-file .zip are also supported. + + ## Introduction If you are completely new to FTP transfers you might benefit from reading a [wikihow](https://www.wikihow.com/Use-FTP) page about it. @@ -22,32 +22,18 @@ client. Please see the [comparison](https://en.wikipedia.org/wiki/Comparison_of_ ## Upload with a client -In this example, FileZilla for MacOS is used. Point your client to the FTP server hostname provided in the upload modal window (`usegalaxy.org` for Galaxy Main). +In this example, FileZilla for MacOS is used. Point your client to the FTP server hostname provided in the upload modal window (e.g. `ftp.usegalaxy.eu` for Galaxy Europe). ![FTP client connection details](./ftp-connect.png) - +If you are having trouble connecting to the server try enabling FTP with `passive` mode in your client. In most clients, when a connection is made with `FTP` or `FTPS`, a pop-up server certificate authentication will need to be accepted. -
- -
- -In this video, the changes for `FTPS` are explained along with how to configure `FTP` client settings and verfify the target server's certificate. - -Below you can see my files copied to the destination on Galaxy's FTP server. -![files uploaded to Galaxy FTP server](./ftp-files.png) - Need more help? See: [Galaxy Help](https://help.galaxyproject.org/) +## Upload using command line - -## Upload with lftp (command line) - +### lftp In this example, `lftp` for MacOS is used. First, check to see if `lftp` is installed. Type in the command and the prompt will result, as show below, *if installed*. Type `exit` at the prompt to back out of the session. @@ -64,21 +50,23 @@ Command-line for `lftp` when connecting to the Public Main Galaxy server. Execut For explicit FTPS: ``` -$ lftp -u user@email.edu usegalaxy.org +$ lftp -u user@email.edu ftp.usegalaxy.example ``` For implicit FTPS: ``` -$ lftp -u user@email.edu ftps://usegalaxy.org +$ lftp -u user@email.edu ftps://ftp.usegalaxy.example ``` -If you are using a different Galaxy server, `FTPS` may or may not be enabled, or the server may only accept implicit or explicit `FTP/FTPS` connections. Check with the administrators of that server if you are not sure. +On some Galaxy servers `FTPS` may or may not be enabled, or the server may only accept implicit or explicit `FTP/FTPS` connections. Check with the administrators of that server if you are not sure. + +### ftp -General `FTP` instructions for a Galaxy server *that has `FTP` enabled but not `FTPS`*. The base URL for the server is used for `othergalaxy.org` in the command below. The `email` (aka `user@email.edu`) and `password` is also server specific and the same as when logging in through a browser. +General `FTP` command for a Galaxy server *that has `FTP` enabled but not `FTPS`* is below. The `email` (aka `user@email.example`) and `password` is also server specific and the same as when logging in through a browser. ``` -$ ftp -u user@email.edu othergalaxy.org +$ ftp -u user@email.example ftp.usegalaxy.example ``` @@ -90,11 +78,10 @@ in the standard upload interface. Select the ones you want to import and hit Sta ![FTP files on the Upload File tool form](./ftp-select.png) -