Background

During the first week of the course you will be doing computer labs using either your own computers or those in the computer room, but accessing resources at UPPMAX (Uppsala Multidisciplinary Centre for Advanced Computational Science). To be able to log-in and use resources at UPPMAX, each student needs to apply for a personal account at SUPR/NAISS and link it to the program/course account that will be used during the course. This may take some time and we need you to prepare this before the course starts. During the course we will be using the program account that is administrated by the programme director of the Master's Programme in Precision Medicine. The project has ID UPPMAX 2024/2-1 and the title “3MG038 - Molekylära tekniker och dataanalys inom precisionsmedicin I”.

Action

Before the start of the course you need to register in SUPR and apply for and get an UPPMAX account that can get access to the program account on the UPPMAX cluster Pelle. This is a two-stage process that is documented on this page: https://docs.uppmax.uu.se/getting_started/get_started/

At first you need to follow the steps, i.e visit the national project management platform SUPR at NAISS., register in SUPR. and accept the user agreement.

With the account you can request membership in the project called "UPPMAX 2024/2-1" that we will be using during the course, instructions: https://docs.uppmax.uu.se/getting_started/join_existing_project/

As soon as you have been granted project membership you will receive an email and you can then proceed.

Remember to test to log in

If you have a Windows computer, you may first install the SSH client MobaXTerm. On Linux and Mac OS, the SSH connection can be done from the default terminal that is already installed.

When you have been given your UPPMAX account and have access to the UPPMAX 2024/2-1 project you should test to log in to the project account on the Pelle cluster at UPPMAX. Support pages from UPPMAX are available here. and specifically there are instructions on how to log in, for different operative systems, here.

Please test to log in before the course starts. If you have problems we will allocate time during the first session on Monday 19^th to make sure everybody can log in.

Download a test file from Pelle to your local computer

The course's materials are located in /crex/proj/uppmax2024-2-1/ and the data for the computer labs in /crex/proj/uppmax2024-2-1/nobackup/lab_files.

Download files and folder with the graphical tool FileZilla

Download the archive with the official executable for your OS from https://filezilla-project.org/download.php?platform=win64 (for Windows 64-bit, you can change the OS by clicking on your platform’s icon under “More download options”) and follow the installation/configuration instructions:
• Windows: https://wiki.filezilla-project.org/Client_Installation#Installing_on_Windows
• Mac OS: https://wiki.filezilla-project.org/Client_Installation#Installing_on_Mac_OS_X
• Ubuntu: decompress the archive to a chosen location, navigate to FileZilla_3.69.5_x86_64-linux-gnu/FileZilla3/bin and run the executable “filezilla”. Note that installing FileZilla via a package manager from an archive repository may work, we could not get that to work though when we tried to follow the instructions.

Once FileZilla was installed on your computer, follow UPPMAX’ instructions: https://docs.uppmax.uu.se/software/pelle_file_transfer_using_filezilla/. You will need to enter your UPPMAX password and TOTP.

Single-file download
Once you have connected to Pelle, navigate to:
• Where you want to save the files on your computer in the “Local site” panel. You can simply double-left-click on the folders.
• The course’s project folder /crex/proj/uppmax2024-2-1/first_week_computer_labs/linux_I in the “Remote site” panel.

Screenshot from 2025-12-23 11-45-38.png

Double-left-click on the file to transfer Homo_sapiens.GRCh38.dna.chromosome.MT.fa.gz, enter your UPPMAX password and TOTP.
Can you see the file locally on your computer now?

Download an entire folder
Navigate 1 level up back to /crex/proj/uppmax2024-2-1/first_week_computer_labs on Pelle. Right-click on the subfolder linux_I in the lower panel and select “Download”. Enter your UPPMAX password and TOTP.

Screenshot from 2025-12-23 11-55-16.png

Can you see the folder locally on your computer now? What can you find in that folder?

Limitations of FileZilla
FileZilla is a suitable tool as long as you need to transfer relatively small files and folders. For larger ones, you must use other alternatives such as the command-line tools `scp` or `rsync`. You will learn more about these commands and experiment with them later in the computer lab `linux_I`.

Various alternative exists to transfer files, they are documented here.

A functionality called “webexport” might also been usable (not tested on Pelle though): https://docs.uppmax.uu.se/cluster_guides/webexport/

Optional: experiment other download alternatives from the command line

1. Make sure you know where the default home directory of your terminal (emulator) is located.
• Linux terminal: /home
• MacOS terminal: /Users
• Windows using MobaXterm (terminal emulator):
◦ https://hpc.ncsu.edu/Documents/mobaxterm.php in the section "Customize the home directory"
◦ https://mobaxterm.mobatek.net/documentation.html#2_2_1 in the section "3. Global settings"
◦ Please change this default location if you want it to be somewhere else, and remember it in case some downloaded files would end up there.

2. Test files to download
Try to download locally some course materials with scp and/or rsync. The whole course directory is too large, but try to transfer:
- a single file, for example `/crex/proj/uppmax2024-2-1/first_week_computer_labs/first_week_computer_labs/linux_I/Homo_sapiens.GRCh38.dna.chromosome.MT.fa.gz` (the file is empty, this is normal)
- an entire folder, for example the materials for the first computer labs: `/crex/proj/uppmax2024-2-1/first_week_computer_labs/linux_I`

Questions

• Can you navigate to the downloaded directory on your file system?
• Try to type a scp command in the terminal on Pelle. What happens?

Additional software

For the various computer labs, you may need the SSH client/terminal emulator MobaXTerm if you are a Windows user. Please install it: https://mobaxterm.mobatek.net/.

For the labs on weeks 2 and 3 of the course we will be using the Integrative Genomics Viewer, IGV (https://igv.org). You can already now test to install it on your computer. Download and install the version that corresponds to your OS at https://igv.org/doc/desktop/#DownloadPage.