gitea-pages/docs/cls/software/modules.md

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
Warp	warp	✓	-	Interactive

Protein Structure Prediction and Design

Software	Module name	CPU/A100 nodes	GH nodes	Run type
AlphaFold 3	alphafold3	✓	✓	Batch job
AlphaFold 2	alphafold24	✓	-	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	Spack13	✓	-	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.sh14	✓	-	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

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

---

1. module use Alps_A100; module load BindCraft ↩︎

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. module use Spack unstable; module load gcc/12.3 openmpi/5.0.7-qhmk-A100-gpu py-pymol/3.1.0-5qcf ↩︎

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