Download NGS data from the FGCZ
Table of contents
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.
- 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:
SFTPRequirement: 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.
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 -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
HTTPSUsing a web-browser (firefox, chrome...) or a command line tool (wget).
$ firefox https://fgcz-gstore.uzh.ch/projects/p403/my_folder/my_file.txt
$ wget --user tanguy --ask-password https://fgcz-gstore.uzh.ch/projects/p403/my_folder/my_file.txt
$ 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/