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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.

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 ✓ ✓ 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

  1. module use Alps_A100; module load BindCraft (A100 GPU nodes) ↩

  2. source /data/project/cls/shared/software/cryosamba/dev_2025_11/cryosamba_module.sh load ↩

  3. module use MX; module load phenix/phenix-1.20-4459 ↩

  4. module use MX; module load alphafold ↩

  5. source /data/project/cls/shared/software/dl_binder_design/1.0.0/dl_binder_design_module.sh proteinmpnn_binder_design ↩

  6. source /data/project/cls/shared/software/dl_binder_design/1.0.0/dl_binder_design_module.sh af2_binder_design ↩

  7. source /data/project/cls/shared/software/rocket/0.2.0/rocket_module.sh load ↩

  8. source /data/project/cls/shared/software/GRASP-JAX/dev_2025_11/GRASP_module.sh load ↩

  9. module use MX; module load Rosetta ↩

  10. source /data/project/cls/shared/software/germinal/dev_2025_10/germinal/germinal_module.sh load ↩

  11. source /data/project/cls/shared/software/BoltzDesign1/dev_2025_07/BoltzDesign1_module.sh load ↩

  12. source /data/project/cls/shared/software/prosculpt/1.1.4/prosculpt_module.sh load ↩

  13. source /data/project/cls/shared/software/DNet/dnet_module.sh load ↩