Download NGS data from the FGCZ

If your project is p403 then all accessible NGS data is found at https://fgcz-gstore.uzh.ch/projects/p403
A link of https://fgcz-gstore.uzh.ch/projects/p403/yourfolder will be translated to the path /srv/gstore/projects/p403/yourfolder on our storage server.
Data is access controlled. Please user your B-Fabric username/password. Available access options are listed below.

For downloading entire folders, do use SFTP.

B-Fabric Downloader

  • If you have Java 1.8 installed, you can use the GUI based download manager.
    • for experts it might be possible to parse the JNLP file and do the download without the need of Java
  • Without Java you can just click on an icon and download single resource or all resources of a workunit at once with your browser
    • Due to security restrictions of browsers and OS, there might be some more clicks needed.

Login to B-Fabric, select the workunits pane on the left and choose your workunit to download.
See B-Fabric User Manual:


Requirement: at least one running or finished project in B-Fabric !!
You can use any FTP client (FileZilla...) or a command line tool.
Please note that B-Fabric users have to use port 666. FGCZ employess can also use the standard port.
SFTP with FileZilla
Protocol: SFTP-SSH File Transfer Protocol
Host: fgcz-gstore.uzh.ch
Port: 666
User: <your B-Fabric username>
Password: <your B-Fabric password>
Once "Connect", you can navigate to the path you want to download. For example: /projects/p403/my_folder

SFTP from the command line
$ sftp  -P 666 <your B-Fabric username>@fgcz-gstore.uzh.ch
ftp> cd /projects/p403/my_folder
ftp> get my_file.txt
ftp> # or
ftp> cd /projects/p403
ftp> get -r my_folder


Using a web-browser (firefox, chrome...) or a command line tool (wget).
Firefox from the command line
$ firefox https://fgcz-gstore.uzh.ch/projects/p403/my_folder/my_file.txt

Wget from the command line, single File
$ wget --user tanguy --ask-password https://fgcz-gstore.uzh.ch/projects/p403/my_folder/my_file.txt

Wget from the command line, Folder
$ wget --user yourUserName -e robots=off --ask-password -r --no-parent -nH --cut-dirs=2 --reject="index.html*" https://fgcz-gstore.uzh.ch/projects/yourProjectNumber/yourDirectory/

Created by tanguy. Last Modification: 2023-03-04 07:24 by schmidt.