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added mriqc workaround
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stebo85 authored Nov 8, 2024
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<!-- markdown-link-check-disable -->
Neurodesk is already installed at UQ's Bunya supercomputer. To access neurodesk tools you need to be in an interactive job (so either start a virtual desktop via Open On-Demand: https://bunya-ondemand.rcc.uq.edu.au/pun/sys/dashboard) or run:
Neurodesk is installed at the University of Queensland's supercomputer "Bunya". To access neurodesk tools you need to be in an interactive job (so either start a virtual desktop via Open On-Demand: https://bunya-ondemand.rcc.uq.edu.au/pun/sys/dashboard) or run:
```
salloc --nodes=1 --ntasks-per-node=1 --cpus-per-task=1 --mem=5G --job-name=TinyInteractive --time=01:00:00 --partition=debug --account=REPLACE_THIS_WITH_YOUR_AccountString srun --export=PATH,TERM,HOME,LANG --pty /bin/bash -l
```
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export TMPDIR=/tmp
```

NOTE: MRIQC has its $HOME variable hardcoded to be /home/mriqc. This leads to problems on Bunya. A workaround is to run this before mriqc:
```
export neurodesk_singularity_opts="--home $HOME:/home"
```

If you are missing an application, please contact [email protected] and ask for the neurodesk installation to be updated on Bunya :)

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