Helix/Software: Difference between revisions
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H Winkhardt (talk | contribs) (added rstan) |
H Schumacher (talk | contribs) (Added mention of Alphafold and Link to BioStructureHub Tutorials) |
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Visit [https://www.bwhpc.de/software.php https://www.bwhpc.de/software.php], select <code>Cluster → bwForCluster Helix</code> |
Visit [https://www.bwhpc.de/software.php https://www.bwhpc.de/software.php], select <code>Cluster → bwForCluster Helix</code> |
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On cluster: <code>module avail</code> |
On the cluster: <code>module avail</code> |
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== Documentation on the Cluster == |
== Documentation on the Cluster == |
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Documentation for environment |
Documentation for each environment module is available on the cluster: |
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* with command <code>module help</code> |
* with command <code>module help</code> |
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* examples are in <code>$<SOFTNAME>_EXA_DIR</code> (batch script + other needed input files). This environment variable is available as soon as the module is loaded. |
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* examples in <code>$SOFTNAME_EXA_DIR</code> |
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** Some modules, e.g. the Alphafold module, include an especially extensive example. |
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== Documentation in the Wiki == |
== Documentation in the Wiki == |
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For some environment modules additional documentation is provided here. |
For some environment modules additional documentation is provided here. |
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* [[Helix/Software/ |
* [[Helix/Software/Singularity | Singularity]] (containers) |
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* [[ |
* [[Development/Conda | Conda]] |
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* [[Python | Python]] |
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* [[Helix/Software/R | R]] |
* [[Helix/Software/R | R]] |
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** [[Helix/Software/R/Rstan | Rstan]] |
** [[Helix/Software/R/Rstan | Rstan]] |
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| ⚫ | |||
* [[Helix/Software/SAS | SAS ]] |
* [[Helix/Software/SAS | SAS ]] |
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| ⚫ | |||
* [[Helix/Software/Stata | Stata]] |
* [[Helix/Software/Stata | Stata]] |
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== External Documentation == |
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* '''BioStructureHub Heidelberg:''' Tutorials are provided for using Helix software modules like Alphafold, RFDiffusion etc. and related software on the Helix cluster and on [[Helix/bwVisu | bwVisu]]. |
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*: → [https://github.com/ssciwr/BioStructureHub/tree/main/docs/tutorials Tutorials] |
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Latest revision as of 17:22, 10 September 2026
Environment Modules
Most software is provided as Environment Modules.
Available Software
Visit https://www.bwhpc.de/software.php, select Cluster → bwForCluster Helix
On the cluster: module avail
Documentation on the Cluster
Documentation for each environment module is available on the cluster:
- with command
module help - examples are in
$<SOFTNAME>_EXA_DIR(batch script + other needed input files). This environment variable is available as soon as the module is loaded.- Some modules, e.g. the Alphafold module, include an especially extensive example.
Documentation in the Wiki
For some environment modules additional documentation is provided here.