# AE@UPPMAX - related documentation

## :open_file_folder: General
- [Linux Tools for Windows Users](/bBoRQt4lRAioRooZS8orlw)
- [SSH keys :key:](/tI_4i6AbTGCZhF9YL2ks3Q)
- [Conda - best practices - UPPMAX](/yfd4YuTEQWGvZsanzFUbsw)
- [conda and mamba on Rackham at UPPMAX](/i7Wp6EVZRfyqUuO2EDMT0w?both)
- [Installing Python modules on Bianca - UPPMAX](/nomUQpn5QYO5cWikM6M8NQ) :snake:
- [Cache conda packages for offline installation](/2WNueUUySwGFc8KAIEBE8g)
- [nextflow on Rackham and Bianca](/HjMsa37-QZm4-fA3t88o_g)
- [uv and pixi on computer centers](/1fy41KPQSri5x3jAVro-ow)
- [MySQL server running as user on Bianca](/IBfvKWn_SIiR67eMz8785g)
- [Copying, backup and archiving data from HPC clusters](/XYFb7L0CQbOaQ3MPFPCUTw)
- [Squashfs as alternative archive format](/3MOyODwdQ8GX8faAmrARnA)
- [Troubleshoot your MobaXterm X11 connection to UPPMAX](/Bd_GALerR6a5r5Jdk1jiZg)
- [User defined signal handler on Rackham (trap)](/IreXPvCZSoOy8Wbhv5Ggzg)
- [Access Control Lists (ACL) on Linux](/ycwtw6TmSJia4lqfWe8VpA)
- [Common options to redirect cache to your project folder](/rhLbddPDTD2My-gyUulT7g)
- [Handy environmental variables for use on Rackham/Bianca](/8CB6QW_RSdKzjD24HkdieA)

## :open_file_folder: Software installation

- [Running Gromacs at UPPMAX](/ZALTb95RSqe-04gblgxwCQ)
- [Running CYSTAL17 on Racham](/xOGW9DXUTvua1itXjfH34w)
- [Running interactive Jupyter notebook on Rackham](/pu4nT4nDSuWiRK5BSX_eoA)
- [arcasHLA at UPPMAX](/N8tFk-MkRS2Br0ykkhkMpQ)
- [TraCeR on Bianca](/P3WbpmHdQfCspjWFz8YHpQ)
- [MUMPS at Rackham (spack)](/N31ggYe4Q1GOq0ZENsx5uA)
- [MUMPS on Rackham - hybrid, no tools](/v7C-O_xsRMa_gGdhNq8Vsg)
- [DFTB+ and CONDA](/X-qzbBPATlWZS7DoH9kbxg)
- [asgal - user installation @UPPMAX](/46KZvKKpQbqFn0pQx_-4SA)
- [Awk workshop: QA 2022.08.29 follow-up](/Io9VoKqyTQKd6lsmgD9ICQ)
- [EasyBuild at UPPMAX](/eh9JDJBCRpOYJEgWhb0Wxg)
- [PartitionFinder with conda on Rackham or Bianca](/1DcM6I7OSNykw7rE4wUnRw)
- [StaPH-B ToolKit](/rnpLP9b7QsCKjdVW8pGKbg)
- [RFDiffusion](/oZOMpKxySzaS6HNs8tPVvA)
- [RIMA on Bianca](/SrjKr1_lS3GBI4fwTK3bDg)
- [BACTpipe](/cesXKVaeSrCI5SZQeesc2g)
- [AIRaster on Rackham/Snowy](/Rl7z_2NBSfCj5ln-m0Mkfw)

## :open_file_folder: Small projects

- [Stat Analysis documentation](/N29dXRqsTDG8tvgrd8luXg)
- [Substitute scientific with common species names in a phylogenetic tree file](/h9TgBZxyR56o-4md4pjQ_g)
- [MD2-lab Conda setup](/Wsu0Ub8zS5CkiYqviUHNwg)
- [CAFE5 on Rackham@UPPMAX](/ySJMdhHYTJOjn0n1jggV8A)
- [Running GenoPredPipe on Bianca](/nzG-U5njQvqPYy4HWSz8-w)
- [Portable BioTools](/dDQCIVx8SOSNUIxdT1hj3Q)

## :link: GitHub
- [UPPMAX-Singularity](https://github.com/pmitev/UPPMAX-Singularity)
- [Teoroo-singularity](https://github.com/pmitev/Teoroo-singularity)

## :open_file_folder: Benchmarks
- [Python numpy performance tests](/Y8HBLlJbTA-m6k7fG7oGZA)

## :e-mail: Contacts:
- [Pavlin Mitev](https://katalog.uu.se/profile/?id=N3-1425)
- [UPPMAX](https://www.uppmax.uu.se/)
- [AE@UPPMAX - related documentation](/8sqXISVRRquPDSw9o1DizQ)

###### tags: `UPPMAX`, `SNIC`, `NAISS`