Scientific Software
Fred Hutch maintains open source scientific software for use with HPC resouces at the center. This site provides an inventory of available software and information about using scientific software. The Hutch uses Easybuild to build and manage software. Easybuild is a software build and installation framework for managing scientific software.
Life Science Software Inventory
Inventory of module class “bio” software modules. This is a subset of all modules that are available. The full list of modules encompesses low level system libraries, math libraries, programming languages, and visualization tools.
Programming Language Modules
Scientific Computing maintains custom builds for R and Python. The custom R and Python modules contain hundreds of packages. The package list is a compilation of user requests. Click on the links bellow to see a list of available builds with a list of modules.
Scientific Software Environment
The user interface for using software is Modules. The module command is used to instantiate a specific software package. Easybuild and Modules provide the tools for using scientific software in a repeatable and documented way.
Software Packages
Easybuild modules are built from toolchains. The toolchain provides the foundation for system level libraries and math libraries. Easybuild software modules names contain the software name-version and the toolchain name used to build the module. Custom reciepies used at the Hutch also have suffix fh to distigue them from other published reciepeis. Once a reciepe is published to this repository it is not changed. If changes have to be made to a package the suffix is versioned. (fh1, fh2, fh3 etc).
Using Modules
Modules can be loaded, unloaded, listed and searched. The
module load command can be abrivated to ml.
Load a Python module
ml Python/3.7.4-foss-2019b-fh1
List currently loaded modules
ml list
Unload all modules
ml purge
Show all available Python modules
ml avail Python
Using Modules in Scripts
Place the following in your bash or sbatch scripts to load modules within your scripts.
source /app/lmod/lmod/init/profile
module load R/4.0.0-foss-2019b
Software Requests
Please send software requests to SciComp support. Requests can be made for additional packages to be added for R, Python and for new software. Packaged modules of R and Python are made as soon as possible after new releases are announced.
Module Usage Report
Most frequently loaded modules. (Jan 1, 2024 -> July 1, 2024)
| Module Name | Count |
|---|---|
| R/4.4.0-gfbf-2023b | 515887 |
| Boost/1.83.0-GCC-13.2.0 | 442110 |
| Eigen/3.4.0-GCCcore-13.2.0 | 442038 |
| R/4.3.3-gfbf-2023b | 410328 |
| fhR/4.3.1-foss-2022b | 315485 |
| Python/3.7.4-foss-2019b-fh1 | 290945 |
| R/4.3.1-gfbf-2022b | 128351 |
| GSL/2.7-GCCcore-12.2.0 | 83736 |
| ImageMagick/7.1.0-53-GCCcore-12.2.0 | 83665 |
| cuDNN/8.4.1.50-CUDA-11.7.0 | 83516 |
| fhR/4.1.2-foss-2021b | 80743 |
| fhR/4.0.4-foss-2020b | 73462 |
| fhR/4.4.0-foss-2023b | 40147 |
| fhR/4.3.3-foss-2023b | 35929 |
| gdc-client/1.6.1-GCCcore-10.2.0 | 34472 |
| R/4.3.0-foss-2022b | 26893 |
| Bowtie2/2.4.2-GCC-10.2.0 | 24845 |
| BEDTools/2.30.0-GCC-11.2.0 | 23939 |
| R/4.2.0-foss-2021b | 23696 |
| BCFtools/1.19-GCC-13.2.0 | 19256 |
| GATK/4.4.0.0-GCCcore-12.2.0-Java-17 | 18423 |
| R/4.2.2-foss-2022b | 17425 |
| fhR/4.2.0-foss-2021b | 16071 |
| MACS2/2.2.9.1-foss-2022b | 14896 |
| PyTorch/1.11.0-foss-2021b-CUDA-11.4.1 | 14791 |
| FastQC/0.11.9-Java-11 | 13491 |
| torchvision/0.13.0-foss-2021b-CUDA-11.4.1 | 13433 |
| Trinity/2.12.0-foss-2020b | 12633 |
| IgBLAST/1.22.0-x64-linux | 12185 |
| OpenSlide/3.4.1-GCCcore-12.3.0-largefiles | 11734 |
| Java/17.0.6 | 8672 |
| SAMtools/1.14-GCC-11.2.0 | 6238 |
| Kent_tools/20201201-linux.x86_64 | 5732 |
| BEDTools/2.30.0-GCC-12.2.0 | 5388 |
| Python/3.8.2-GCCcore-9.3.0 | 5381 |
| Bowtie2/2.4.4-GCC-11.2.0 | 4941 |
| Miniconda3/4.9.2 | 4840 |
| SAMtools/1.11-GCC-10.2.0 | 4519 |
| BEDTools/2.29.2-GCC-9.3.0 | 4020 |
| Anaconda3/2023.09-0 | 3821 |
| cutadapt/4.1-GCCcore-11.2.0 | 3791 |
| SAMtools/1.16.1-GCC-11.2.0 | 3583 |
| Java/11.0.2 | 3542 |
| deepTools/3.5.4.post1-gfbf-2022b | 3512 |
| Apptainer/1.1.6 | 3478 |
| SAMtools/1.10-GCCcore-8.3.0 | 2556 |
| openslide-python/1.1.2-GCCcore-11.2.0 | 2527 |
| picard/2.18.29-Java | 2358 |
| fhPython/3.9.6-foss-2021b | 1994 |
| picard/2.21.6-Java-11 | 1851 |
| SAMtools/1.17-GCC-12.2.0 | 1733 |
| STAR/2.7.7a-GCC-10.2.0 | 1711 |
| GATK/4.2.6.1-GCCcore-11.2.0 | 1638 |
| Anaconda3/2020.02 | 1621 |
| GATK/4.1.8.1-GCCcore-8.3.0-Java-11 | 1466 |
| SRA-Toolkit/3.0.0-ubuntu64 | 1458 |
| scikit-learn/1.0.1-foss-2021b | 1404 |
| deepTools/3.5.1-foss-2021b | 1331 |
| picard/2.6.0-Java-11 | 1325 |
| SAMtools/1.19.2-GCC-13.2.0 | 1316 |
| PostgreSQL/10.3-foss-2019b | 1121 |
| Java/21.0.2 | 1111 |
| CUDA/12.1.1 | 1046 |
| MACS2/2.2.6-foss-2019b-Python-3.7.4 | 1024 |
| STAR/2.7.10b-GCC-12.2.0 | 1023 |
| CellRanger/8.0.0 | 1004 |
| PyTorch/1.12.1-foss-2022a-CUDA-11.7.0 | 1002 |
| matplotlib/3.5.2-foss-2022a | 974 |
| BLAST+/2.14.0-gompi-2022b | 894 |
| Python/3.10.8-GCCcore-12.2.0 | 874 |
| Nextflow/23.04.2 | 755 |
| Singularity/3.5.3 | 750 |
| picard/2.25.1-Java-11 | 727 |
| Kraken2/2.1.3-gompi-2022b | 701 |
| seqtk/1.3-GCC-10.2.0 | 655 |
| GATK/4.2.5.0-GCCcore-11.2.0-Java-11 | 652 |
| BWA/0.7.17-GCCcore-11.2.0 | 613 |
| SlamDunk/0.4.3-foss-2021b | 606 |