115 lines
10 KiB
Markdown
115 lines
10 KiB
Markdown
# Modules available
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This page provides a list of the modules available on the cluster. The list may differ from the modules currently installed on the **Merlin 7** cluster.
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!!! tip "Finding the right module"
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If you need a specific software package or version, use `module avail` or `module spider` to check which versions are available before loading the module.
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To load a module, run: `module load [module_name]`
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## Electron Microscopy
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| Software | Module name | CPU/A100 nodes | GH nodes | Run type |
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| ------------- | ---------------- | :-------------: | :-------------------: | ---------------------- |
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| CryoSPARC | - | ✓ | ✓ | Batch job |
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| RELION | `relion` | ✓ | ✓ (IMOD not available) | Interactive, Batch job |
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| LipIDens | `lipidens` | ✓ | ✓ | Interactive |
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| ModelAngelo | `model_angelo` | ✓ | ✓ | Batch job |
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| BindCraft | `BindCraft`[^1] | ✓ | ✓ | Batch job |
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| CryoDECO | `cryodeco` | ✓ | - | Batch job |
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| CryoRanker | `cryo_ief` | ✓ | - | Batch job |
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| Cryo-IEF | `cryo_ief` | ✓ | - | Batch job |
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| CryoSamba | `cryosamba`[^2] | ✓ | - | Interactive |
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| crYOLO | `crYOLO` | ✓ | - | Interactive, Batch job |
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| CryoDRGN | `cryodrgn` | ✓ | - | Batch job |
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| pyEM | `pyem` | ✓ | - | Batch job |
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| Phenix | `phenix`[^3] | ✓ | - | Interactive |
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| MotionCor3 | `MotionCor3` | ✓ | ✓ | Batch job |
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| AreTomo3 | `AreTomo3` | ✓ | - | Batch job |
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| AreTomo2 | `AreTomo2` | ✓ | ✓ | Batch job |
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| spIsoNet | `spIsoNet` | ✓ | - | Batch job |
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| IsoNet | `IsoNet` | ✓ | - | Interactive, Batch job |
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| IsoNet2 | `IsoNet2` | ✓ | - | Batch job |
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| Warp | `warp` | ✓ | - | Interactive |
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| ctffind4 | `ctffind4` | ✓ | ✓ | Batch job |
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| ResMap | `ResMap` | ✓ | ✓ | Interactive, Batch job |
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| pytom-match-pick | `pytom-match-pick` | ✓ | ✓ | Batch job |
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| topaz | `topaz` | ✓ | ✓ | Batch job |
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## Protein Structure Prediction and Design
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| Software | Module name | CPU/A100 nodes | GH nodes | Run type |
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| ----------------- | ------------------------------------ | :-------------: | :-------------------: | ---------------------- |
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| AlphaFold 3 | `alphafold3` | ✓ | ✓ | Batch job |
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| AlphaFold 2 | `alphafold`[^4] | ✓ | - | Batch job |
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| dl_binder_design | dl_binder_design_module.sh [^5],[^6] | ✓ | - | Batch job |
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| ROCKET | rocket_module.sh [^7] | ✓ | - | Batch job |
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| GRASP-JAX | GRASP_module.sh [^8] | ✓ | - | Batch job |
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| Rosetta | `Rosetta`[^9] | ✓ | ✓ | Batch job |
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| Germinal | germinal_module.sh[^10] | ✓ | - | Batch job |
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| Chai-1 | `chai-1` | ✓ | ✓ | Batch job |
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| Boltz-2 | `boltz` | ✓ | ✓ | Batch job |
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| BoltzDesign1 | BoltzDesign1_module.sh[^11] | ✓ | - | Interactive, Batch job |
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| RFdiffusion | `RFdiffusion` | ✓ | - | Batch job |
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| ProteinMPNN | `ProteinMPNN` | ✓ | - | Batch job |
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| prosculpt | prosculpt_module.sh[^12] | ✓ | - | Interactive, Batch job |
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| ColabFold | `colabfold` | ✓ | - | Batch job |
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| AF3x | `af3x` | ✓ | - | Batch job |
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## Molecular and Volumetric Visualization
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| Software | Module name | CPU/A100 nodes | GH nodes | Run type |
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| ----------------- | ------------------- | :-------------: | :-------------------: | ---------------------- |
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| ChimeraX | `chimerax` | ✓ | - | Interactive |
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| IMOD | `IMOD` | ✓ | - | Interactive, Batch job |
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| MemBrain | `membrain` | ✓ | - | Interactive, Batch job |
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| PyMOL | `pymol` | ✓ | - | Interactive |
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| napari | `napari` | ✓ | - | Interactive |
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| napari-boxmanager | `napari-boxmanager` | ✓ | - | Interactive |
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| napari-tomoslice | `napari-tomoslice` | ✓ | - | Interactive |
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## Molecular Dynamics
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| Software | Module name | CPU/A100 nodes | GH nodes | Run type |
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| ------------- | ------------------- | :-------------: | :-------------------: | ---------------------- |
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| DNet | dnet_module.sh[^13] | ✓ | - | Interactive, Batch job |
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| NAMD | `NAMD` | ✓ | ✓ | Batch job |
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| VMD | `vmd` | ✓ | - | Interactive |
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| GROMACS | `gromacs` | ✓ | ✓ | Batch job |
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| Amber26 | `amber` | ✓ | ✓ | Batch job |
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| AmberTools26 | `ambertools` | ✓ | - | Batch job |
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| PLUMED | `plumed` | ✓ | ✓ | Batch job |
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| LAMMPS | `lammps` | ✓ | ✓ | Batch job |
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| SevenNet | `sevennet` | ✓ | ✓ | Batch job |
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| dssp | `dssp` | ✓ | ✓ | Batch job |
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## Bioinformatics
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| Software | Module name | CPU/A100 nodes | GH nodes | Run type |
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| ------------- | ---------------- | :-------------: | :-------------------: | ---------------------- |
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| FastQC | `fastqc` | ✓ | - | Batch job |
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| SRA Toolkit | `sratoolkit` | ✓ | - | Batch job |
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| Entrez Direct | `edirect` | ✓ | - | Batch job |
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| Cell Ranger | `cellranger` | ✓ | - | Batch job |
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| kalign | `kalign` | ✓ | ✓ | Batch job |
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| Refgenie | `refgenie` | ✓ | ✓ | Interactive |
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| Nextflow | `nextflow` | ✓ | ✓ | Interactive, Batch job |
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| nf-core | `nf-core` | ✓ | ✓ | Interactive, Batch job |
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| hh-suite | `hhsuite` | ✓ | ✓ | Batch job |
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| hmmer | `hmmer` | ✓ | ✓ | Batch job |
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| SeqKit | `seqkit` | ✓ | - | Batch job |
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[^1]: `module use Alps_A100; module load BindCraft` (A100 GPU nodes)
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[^2]: `source /data/project/cls/shared/software/cryosamba/dev_2025_11/cryosamba_module.sh load`
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[^3]: `module use MX; module load phenix/phenix-1.20-4459`
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[^4]: `module use MX; module load alphafold`
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[^5]: `source /data/project/cls/shared/software/dl_binder_design/1.0.0/dl_binder_design_module.sh proteinmpnn_binder_design`
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[^6]: `source /data/project/cls/shared/software/dl_binder_design/1.0.0/dl_binder_design_module.sh af2_binder_design`
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[^7]: `source /data/project/cls/shared/software/rocket/0.2.0/rocket_module.sh load`
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[^8]: `source /data/project/cls/shared/software/GRASP-JAX/dev_2025_11/GRASP_module.sh load`
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[^9]: `module use MX; module load Rosetta`
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[^10]: `source /data/project/cls/shared/software/germinal/dev_2025_10/germinal/germinal_module.sh load`
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[^11]: `source /data/project/cls/shared/software/BoltzDesign1/dev_2025_07/BoltzDesign1_module.sh load`
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[^12]: `source /data/project/cls/shared/software/prosculpt/1.1.4/prosculpt_module.sh load`
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[^13]: `source /data/project/cls/shared/software/DNet/dnet_module.sh load`
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