How can I upload and download files from UPPMAX to my computer?

Transfering files to and from your UPPMAX is one of the things we get asked about most. Regardless what operating system or application you use, all connections (including transfer) to UPPMAX muse be made over a secure SSH-connection. Below we have listed for each operating system a couple of ways to transfer your files.

Note: You want to transfer from abroad? Please read this guide first. 

Linux and OS X

The rsync tool is available on both Linux and Mac OS X systems and is one of our favourite tools. It is a command-line based fast, versatile and remote file-copying tool. The best thing about it that it can restart a lost connection without copying all files again. That is very handy! The rsync tool is available from the Terminal, which you can search and find from the Launchpad if you are using OS X. For more information on rsync please read the manual ("man rsync") or search for guides on the Internet. There are plenty of information available.

A standard rsync command call looks like this

rsync -flags user@cluster.uppmax.uu.se:/path/to/your/files destination_directory

where -flags is rsync options, and user is your UPPMAX username. Perhaps best explained by a few examples:

Example 1: Transfering files from UPPMAX

rsync -ah jvneumann@rackham.uppmax.uu.se:/proj/snic2017-1-1/nature_pub ~/

The above command connects to the Rackham cluster as user jvneumann and transfer the directory /proj/snic2017-1-1/nature_pub back to my home (~) directory on my machine. If I have not set-up passwordless login I will be prompted to enter my password. The flag "-ah" is short for -a (archive) and -h (human readable, for some nicer formatting).

Example 2:  Transfering files to UPPMAX

rsync -ah new_data_dir jwatson@milou.uppmax.uu.se:/proj/b20170101/

Will transfer the directory new_data_dir to the project directory b20170101

For Mac OS X users, if you are having trouble with rsync then the SFTP client Cyberduck is an alternative for graphically browsing and uploading/downloading files. Download it from http://cyberduck.ch/ and follow their instructions to install it on your computer.

Windows

You can use the WinSCP program or MobaXTerm to work with files on UPPMAX.

Please note that when you first login to UPPMAX you will see your home directory. If you are an UPPNEX user and want to access your UPPNEX project's data files then you need to browse to the directory /proj/[project id]/. You can read more about our different file systems and quota limits on our disk storage guide.

Another alternative is to mount e.g. your UPPMAX home directory on your local machine as a network drive using SSHFS. While convenient, it can be tricky to set up and we will not provide support, so we leave the details as an exercise for the reader.

Transfers to NCBI or ENA

Data uploaded to the Nucleotide Archive (ENA) is reflected to NCBI, vice versa. We recommend uploading data to ENA from UPPMAX. Please follow this guide: https://ena-docs.readthedocs.io/en/latest/submit/general-guide.html