:::danger Disclaimer: The purpose of the transit server is to transfer files to/from the wharf area in your sensiteve project. This tutorial is not an official documentation and does not give a guarantee that it will work for any case. If you experience problems following this material - please apply for small project on Rackham and use Rackham for this purpose. ::: :::warning Keep in mind that your $HOME folder is a read-only snapshot of your Rackham $HOME folder and has limit of 1.3GB write overlayer. df -h | grep $USER overlay 1.3G 4.0K 1.3G 1% /domus/h1/XXXXX :::

:::danger Disclaimer: The purpose of the transit server is to transfer files to/from the wharf area in your sensiteve project. This tutorial is not an official documentation and does not give a guarantee that it will work for any case. If you experience problems following this material - please apply for small project on Rackham and use Rackham for this purpose. ::: :::warning Keep in mind that your $HOME folder is a read-only snapshot of your Rackham $HOME folder and has limit of 1.3GB write overlayer. df -h | grep $USER overlay 1.3G 4.0K 1.3G 1% /domus/h1/XXXXX :::

:::danger Disclaimer: Instructions below assume that conda provided by the module system is working. Please, submit a support request if something does not work or you want to know why is not working. ::: :::success Alternatively - follow this tutorial on how to install own conda on Rackham. ::: The default conda module is not complete setup and will, by default, cache and install in your $HOME folder which is only 32GB and pretty much, not enough for anything. Follow the instructions below to redirect conda cache and environments to your project folder. Prepare your conda setup.

:::danger The nf-core pipelines are not supported anymore at UPPMAX. To learn how to download your pipeline for offline use on Bianca, please follow this tutorial nf-core pipelines on Bianca instead. ::: 1. Available modules i. Load the bioinfo-tools module tree $ module load bioinfo-tools ii. Related modules and versions as of 2023.04.24

https://cubids.readthedocs.io/en/latest/ Running CuBIDS on Bianca Make sure you have the 'cubids.sif' container somewhere in your project folder. #cd to where is your data cd ... # Start a shell in the container. Replace with the full path. apptainer shell /full_path_to/cubids.sif

https://code.visualstudio.com/docs/remote/faq#_can-i-run-vs-code-server-on-older-linux-distributions Starting with VS Code release 1.99 (March 2025), the prebuilt servers distributed by VS Code are only compatible with Linux distributions that are based on glibc 2.28 or later. These include for example, Debian 10, RHEL 8, or Ubuntu 20.04. To continue running newer version of VSCode remotely over SSH on Rackham, please, add these 3 lines into your ~/.bashrc on Rackham. export VSCODE_SERVER_CUSTOM_GLIBC_LINKER=/sw/apps/pm-tools/latest/rackham/x86_64-gcc-8.5.0-glibc-2.28/x86_64-linux-gnu/x86_64-linux-gnu/sysroot/lib/ld-2.28.so export VSCODE_SERVER_CUSTOM_GLIBC_PATH=/sw/apps/pm-tools/latest/rackham/x86_64-gcc-8.5.0-glibc-2.28/x86_64-linux-gnu/x86_64-linux-gnu/sysroot/lib:/lib64 export VSCODE_SERVER_PATCHELF_PATH=/sw/apps/pm-tools/glibc-2.28/patchelf Contacts:

Before connecting to Rackham Quite often, the problem is on the client side and it is not related to the remote computer or the connection to it.Please check the points below to establish that the local setup is working fine. Make sure the MobaXterm X server is running.The icon in the top right should be colorful for running and grayed out when is not running. Check that the X11 server is enabled in the settings. Check that you have X11-Forwarding option enabled. Check that your local MobaXterm terminal can communicate with the MobaXterm X server.

Load conda source /sw/apps/conda/latest/rackham_stage/etc/profile.d/conda.sh Delete old environment, if necessary conda env list conda env remove -n spipe Install complete environment environment.yml channels: - file:///sw/apps/conda/latest/rackham/local_repo/conda-forge

:open_file_folder: General Linux Tools for Windows Users SSH keys :key: Conda - best practices - UPPMAX conda and mamba on Rackham at UPPMAX Installing Python modules on Bianca - UPPMAX :snake: Cache conda packages for offline installation nextflow on Rackham and Bianca uv and pixi on computer centers MySQL server running as user on Bianca

Create an SSH key pair with the following command:​​​​ssh-keygen -o -a 100 -t ed25519 -f ~/.ssh/id_ed25519_key -C "MyNewKey" Add your newly generated Ed25519 key to an SSH agent:​​​​ssh-add ~/.ssh/id_ed25519_key Copy the public key to Rackham or other server.​​​​ssh-copy-id -i .ssh/id_ed25519_key.pub rackham.uppmax.uu.se Connect​​​​ssh username@rackham.uppmax.uu.se On Bianca Add the content of your public key id_ed25519_key.pub to $HOME/.ssh/authorized_keys. You can not use the same command ssh-copy as in the case for Rackham i.e. you have to manually bring the key on Bianca.

https://github.com/kevinjohncutler/omnipose There are several dependencies that are difficult to provide on some of the systems unless installed with root. Rackham runs discontinued CentoOS 7 (until replaced by Pelle) and has libc version 2.27 which is too old to be supported by new software. Pelle will run Rocky 9 which currently have libc version 2.35. Common way to "shift" this problem is to run a container which can provide the necessary libraries and dependencies. Installing omnipose The tool requires a lot of dependencies and the project is "poisoned" by braking dependencies. On 2025.01.29 the following is installing successfully on Linux amd64 platform regardless of the distribution. https://hackmd.io/@pmitev/conda_on_Rackham

:::danger Note: the following instructions do not apply for Bianca! ::: In case you insist using conda from the module system, please follow these instructions. Conda - best practices @ UPPMAX If you experience unexpected problems with the conda provided by the module system on Rackham or anaconda3 on Dardel, you can easily install your own and maintain it yourself. :exclamation:Important: Please, install miniforge3 or miniconda3 in your project folder!:exclamation:

Bianca is a research system dedicated for analyzing sensitive personal data from large-scale molecular experiments. Bianca is part of the SNIC-SENS project. Since Bianca is designed to handle sensitive personal data security is a key aspect of the configuration and features restricted access and lack of direct Internet access to and from the cluster. This make it particularly difficult to use common tools to maintain python modules or software installations. Here are some tips and advises on different way to approach the problem. User installs via pip pip documentation Download the necessary modules - docs.

:::info These instructions install nextflow and nf-core in your $HOME folder since they are relatively small. Please, consider installing any tool or software in your project folder instead. ::: :::success UPDATE 2024.10.23: nextflow is available as module so you can use that one if you choose so. module load PDC nextflow apptainer python/3.12.3 ::: :gear: General setup

https://vireosnp.readthedocs.io/en/latest/install.html Login on transit.uppmax.uu.se https://uppmax.github.io/UPPMAX-documentation/cluster_guides/transit/ On transit # Mount the wharf project folder in your home folder mount_wharf sensXXXXXX # Enter the wharf directory cd sensXXXXXX

or any other cluster running SLURM and Singularity/Apptainer General setup # Load relevant modules $ module load PDC/23.12 java/17.0.4 singularity anaconda3 # make bin folder and add "export PATH+=$HOME/bin" in ~/.bashrc $ mkdir -p $HOME/bin $ cd $HOME/bin $ export PATH+=:$HOME/bin

https://komorowskilab.github.io/R.ROSETTA/tutorials.html#installation To run on Bianca The instructions to run anywhere else should be the same, except that when Internet is available, wine could work without installing wine-mono. # Get a shell in the container environment singularity shell /sw/apps/pm-tools/latest/rackham/singularity/R.ROSETTA/rosetta.sif # On Bianca, Wine struggles to run without .NET which is not a problem if there is an Internet

https://github.com/PacificBiosciences/HiFi-16S-workflow Login to transit.uppmax.uu.se Documentation:https://uppmax.github.io/UPPMAX-documentation/cluster_guides/transfer_bianca/#transit-server Mount the wharf of your project. ​​​​user@transit:~$ mount_wharf sens2023531 ​​​​Mounting wharf (accessible for you only) to /home/<user>/sens2023531 ​​​​<user>-sens2023531@bianca-sftp.uppmax.uu.se's password:

# Change to fit your account PRJ_DIR=/crex/uppmax2022-0-00 # general export XDG_CACHE_HOME=${PRJ_DIR}/nobackup/XDG_CACHE_HOME mkdir -p $XDG_CACHE_HOME # Singularity export SINGULARITY_CACHEDIR=${PRJ_DIR}/nobackup/SINGULARITY_CACHEDIR export SINGULARITY_TMPDIR=${PRJ_DIR}/nobackup/SINGULARITY_TMPDIR

This setup works on any computer with installed Singularity/Apptainer. Avalable on Rackham/Bianca: /sw/apps/pm-tools/latest/rackham/singularity/BioTools/bin Dardel: /pdc/software/uppmax_legacy/pm-tools/singularity/BioTools/bin Tools in the container Note: some tool names are different in the container Name