10 KiB
Modules available
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.
!!! tip "Finding the right module"
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.
To load a module, run: module load [module_name]
Electron Microscopy
| Software | Module name | CPU/A100 nodes | GH nodes | Run type |
|---|---|---|---|---|
| CryoSPARC | - | ✓ | ✓ | Batch job |
| RELION | relion |
✓ | ✓ (IMOD not available) | Interactive, Batch job |
| LipIDens | lipidens |
✓ | ✓ | Interactive |
| ModelAngelo | model_angelo |
✓ | ✓ | Batch job |
| BindCraft | BindCraft1 |
✓ | ✓ | Batch job |
| CryoDECO | cryodeco |
✓ | - | Batch job |
| CryoRanker | cryo_ief |
✓ | - | Batch job |
| Cryo-IEF | cryo_ief |
✓ | - | Batch job |
| CryoSamba | cryosamba2 |
✓ | - | Interactive |
| crYOLO | crYOLO |
✓ | - | Interactive, Batch job |
| CryoDRGN | cryodrgn |
✓ | - | Batch job |
| pyEM | pyem |
✓ | - | Batch job |
| Phenix | phenix3 |
✓ | - | Interactive |
| MotionCor3 | MotionCor3 |
✓ | ✓ | Batch job |
| AreTomo3 | AreTomo3 |
✓ | - | Batch job |
| AreTomo2 | AreTomo2 |
✓ | ✓ | Batch job |
| spIsoNet | spIsoNet |
✓ | - | Batch job |
| IsoNet | IsoNet |
✓ | - | Interactive, Batch job |
| IsoNet2 | IsoNet2 |
✓ | - | Batch job |
| Warp | warp |
✓ | - | Interactive |
| ctffind4 | ctffind4 |
✓ | ✓ | Batch job |
| ResMap | ResMap |
✓ | ✓ | Interactive, Batch job |
| pytom-match-pick | pytom-match-pick |
✓ | ✓ | Batch job |
| topaz | topaz |
✓ | ✓ | Batch job |
Protein Structure Prediction and Design
| Software | Module name | CPU/A100 nodes | GH nodes | Run type |
|---|---|---|---|---|
| AlphaFold 3 | alphafold3 |
✓ | ✓ | Batch job |
| AlphaFold 2 | alphafold4 |
✓ | - | Batch job |
| dl_binder_design | dl_binder_design_module.sh 5 ,6 | ✓ | - | Batch job |
| ROCKET | rocket_module.sh 7 | ✓ | - | Batch job |
| GRASP-JAX | GRASP_module.sh 8 | ✓ | - | Batch job |
| Rosetta | Rosetta9 |
✓ | ✓ | Batch job |
| Germinal | germinal_module.sh10 | ✓ | - | Batch job |
| Chai-1 | chai-1 |
✓ | ✓ | Batch job |
| Boltz-2 | boltz |
✓ | ✓ | Batch job |
| BoltzDesign1 | BoltzDesign1_module.sh11 | ✓ | - | Interactive, Batch job |
| RFdiffusion | RFdiffusion |
✓ | - | Batch job |
| ProteinMPNN | ProteinMPNN |
✓ | - | Batch job |
| prosculpt | prosculpt_module.sh12 | ✓ | - | Interactive, Batch job |
| ColabFold | colabfold |
✓ | - | Batch job |
| AF3x | af3x |
✓ | - | Batch job |
Molecular and Volumetric Visualization
| Software | Module name | CPU/A100 nodes | GH nodes | Run type |
|---|---|---|---|---|
| ChimeraX | chimerax |
✓ | - | Interactive |
| IMOD | IMOD |
✓ | - | Interactive, Batch job |
| MemBrain | membrain |
✓ | - | Interactive, Batch job |
| PyMOL | pymol |
✓ | - | Interactive |
| napari | napari |
✓ | - | Interactive |
| napari-boxmanager | napari-boxmanager |
✓ | - | Interactive |
| napari-tomoslice | napari-tomoslice |
✓ | - | Interactive |
Molecular Dynamics
| Software | Module name | CPU/A100 nodes | GH nodes | Run type |
|---|---|---|---|---|
| DNet | dnet_module.sh13 | ✓ | - | Interactive, Batch job |
| NAMD | NAMD |
✓ | ✓ | Batch job |
| VMD | vmd |
✓ | - | Interactive |
| GROMACS | gromacs |
✓ | ✓ | Batch job |
| Amber26 | amber |
✓ | ✓ | Batch job |
| AmberTools26 | ambertools |
✓ | - | Batch job |
| PLUMED | plumed |
✓ | ✓ | Batch job |
| LAMMPS | lammps |
✓ | ✓ | Batch job |
| SevenNet | sevennet |
✓ | ✓ | Batch job |
| dssp | dssp |
✓ | ✓ | Batch job |
Bioinformatics
| Software | Module name | CPU/A100 nodes | GH nodes | Run type |
|---|---|---|---|---|
| FastQC | fastqc |
✓ | - | Batch job |
| SRA Toolkit | sratoolkit |
✓ | - | Batch job |
| Entrez Direct | edirect |
✓ | - | Batch job |
| Cell Ranger | cellranger |
✓ | - | Batch job |
| kalign | kalign |
✓ | ✓ | Batch job |
| Refgenie | refgenie |
✓ | ✓ | Interactive |
| Nextflow | nextflow |
✓ | ✓ | Interactive, Batch job |
| nf-core | nf-core |
✓ | ✓ | Interactive, Batch job |
| hh-suite | hhsuite |
✓ | ✓ | Batch job |
| hmmer | hmmer |
✓ | ✓ | Batch job |
| SeqKit | seqkit |
✓ | - | Batch job |
-
module use Alps_A100; module load BindCraft(A100 GPU nodes) ↩︎ -
source /data/project/cls/shared/software/cryosamba/dev_2025_11/cryosamba_module.sh load↩︎ -
module use MX; module load phenix/phenix-1.20-4459↩︎ -
module use MX; module load alphafold↩︎ -
source /data/project/cls/shared/software/dl_binder_design/1.0.0/dl_binder_design_module.sh proteinmpnn_binder_design↩︎ -
source /data/project/cls/shared/software/dl_binder_design/1.0.0/dl_binder_design_module.sh af2_binder_design↩︎ -
source /data/project/cls/shared/software/rocket/0.2.0/rocket_module.sh load↩︎ -
source /data/project/cls/shared/software/GRASP-JAX/dev_2025_11/GRASP_module.sh load↩︎ -
module use MX; module load Rosetta↩︎ -
source /data/project/cls/shared/software/germinal/dev_2025_10/germinal/germinal_module.sh load↩︎ -
source /data/project/cls/shared/software/BoltzDesign1/dev_2025_07/BoltzDesign1_module.sh load↩︎ -
source /data/project/cls/shared/software/prosculpt/1.1.4/prosculpt_module.sh load↩︎ -
source /data/project/cls/shared/software/DNet/dnet_module.sh load↩︎