AE@UPPMAX - related documentation

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General

• Linux Tools for Windows Users
• SSH keys
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• Conda - best practices - UPPMAX
• conda and mamba on Rackham at UPPMAX
• Installing Python modules on Bianca - UPPMAX
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• Cache conda packages for offline installation
• nextflow on Rackham and Bianca
• uv and pixi on computer centers
• MySQL server running as user on Bianca
• Copying, backup and archiving data from HPC clusters
• Squashfs as alternative archive format
• Troubleshoot your MobaXterm X11 connection to UPPMAX
• User defined signal handler on Rackham (trap)
• Access Control Lists (ACL) on Linux
• Common options to redirect cache to your project folder
• Handy environmental variables for use on Rackham/Bianca

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Software installation

• Running Gromacs at UPPMAX
• Running CYSTAL17 on Racham
• Running interactive Jupyter notebook on Rackham
• arcasHLA at UPPMAX
• TraCeR on Bianca
• MUMPS at Rackham (spack)
• MUMPS on Rackham - hybrid, no tools
• DFTB+ and CONDA
• asgal - user installation @UPPMAX
• Awk workshop: QA 2022.08.29 follow-up
• EasyBuild at UPPMAX
• PartitionFinder with conda on Rackham or Bianca
• StaPH-B ToolKit
• RFDiffusion
• RIMA on Bianca
• BACTpipe
• AIRaster on Rackham/Snowy

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Small projects

• Stat Analysis documentation
• Substitute scientific with common species names in a phylogenetic tree file
• MD2-lab Conda setup
• CAFE5 on Rackham@UPPMAX
• Running GenoPredPipe on Bianca
• Portable BioTools

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GitHub

• UPPMAX-Singularity
• Teoroo-singularity

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Benchmarks

• Python numpy performance tests

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Contacts:

• Pavlin Mitev
• UPPMAX
• AE@UPPMAX - related documentation

tags: UPPMAX, SNIC