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. (Oct 3, 2022 - Apr 3, 2023)

Name Count Percent
R 1,431,523 39.443534
fhR 1,253,561 34.540050
BCFtools 549,348 15.136485
Java 71,586 1.972448
picard 36,661 1.010141
Python 32,381 0.892211
SAMtools 24,188 0.666465
BEDTools 20,939 0.576944
deepTools 16,995 0.468273
Bowtie2 16,891 0.465407
GATK 10,888 0.300003
Kent_tools 10,266 0.282865
Kraken2 9,188 0.253162
beagle-lib 8,806 0.242637
FastQC 8,787 0.242113
STAR 8,286 0.228309
MUMmer 7,857 0.216488
cutadapt 6,010 0.165597
Anaconda3 5,627 0.155044
Trinity 5,123 0.141157
PLINK2 4,997 0.137685
Singularity 4,994 0.137602
IgBLAST 4,393 0.121043
fhPython 3,903 0.107541
Pandoc 3,835 0.105668
Arriba 3,152 0.086849
BWA 3,003 0.082743
SRA-Toolkit 2.468 0.068002
QUAST 2.300 0.063373
RStudio-Server 2.290 0.063098
Beast 2,084 0.057420
tmux 2,057 0.056676
BLAST+ 1,775 0.048906
MACS2 1,612 0.044415
HTSeq 1,569 0.043230
libGLU 1,554 0.042817
Nextflow 1,469 0.040475
TensorFlow 1,262 0.034772
Emacs 1,251 0.034469
CellRanger 1,200 0.033063
strelka 1,153 0.031768
fgbio 1,121 0.030887
rstudio-server 1,113 0.030666
Subread 1,089 0.030005
Trimmomatic 1,087 0.029950
CNVkit 1,053 0.029013
scanpy 1,044 0.028765
XGBoost 1,004 0.027663
PLINK 910 0.025073
foss 900 0.024798
kallisto 894 0.024632
git 874 0.024081
fhDev 805 0.022180
X11 793 0.021849
GLPK 750 0.020665
OptiType 736 0.020279
PCRE2 659 0.018157
Perl 644 0.017744
OpenBLAS 642 0.017689
CMake 616 0.016973
Automake 607 0.016725
MariaDB 596 0.016421
Pysam 591 0.016284
ncurses 585 0.016118
HISAT2 580 0.015981
libreadline 574 0.015815
cURL 572 0.015760
flex 561 0.015457
Bison 561 0.015457
pkg-config 559 0.015402
texinfo 558 0.015374
libtool 558 0.015374
bsddb3 558 0.015374
PCRE 558 0.015374
DB 558 0.015374
parallel 555 0.015292
tbb 554 0.015264
itpp 554 0.015264
Trim_Galore 553 0.015237
datamash 540 0.014879
RNA-SeQC 531 0.014631
Bowtie 514 0.014162
cuDNN 475 0.013088
gnuplot 452 0.012454
snakemake 447 0.012316
DIAMOND 414 0.011407
BBMap 387 0.010663
IPython 377 0.010387
nextflow 370 0.010195
FLASH 324 0.008927
gatk 283 0.007797
bcl2fastq2 262 0.007219
GLib 256 0.007054
JupyterLab 249 0.006861
Mesa 248 0.006833
GSL 248 0.006833
HLA-HD 247 0.006806
GTK3 247 0.006806
PEAR 222 0.006117
MATLAB 217 0.005979

Modules ranked by most unique users

Splunk Query: index = syslog LMOD: top=yes | stats dc(user) as Users by name | sort - Users

Name Users
R 175
RStudio-Server 133
Python 122
fhR 121
SAMtools 102
Singularity 67
fhPython 57
Anaconda3 54
FastQC 46
BEDTools 44
Java 44
Bowtie2 43
picard 40
CellRanger 37
SRA-Toolkit 34
STAR 34
OpenBLAS 31
BCFtools 28
GATK 28
awscli 28
BWA 25
Nextflow 25
MariaDB 24
cutadapt 24
nextflow 24
CMake 23
deepTools 23
JupyterLab 21
Perl 21
bcl2fastq2 21
MACS2 19
MultiQC 18
foss 18
snakemake 18
tabix 18
cURL 17
tmux 17
X11 16
cellranger 16
rstudio 16
“Kent_tools” 15
Pysam 15
“Trim_Galore” 15
GCC 14
cromwell 14
“rstudio-server” 14
TensorFlow 13
“BLAST+” 12
Automake 11
IGV 11
Miniconda3 11
PCRE2 11
libreadline 11
ncurses 11
plink 11
“Aspera-Connect” 10
BBMap 10
Beast 10
Bison 10
GCCcore 10
HISAT2 10
MATLAB 10
OptiType 10
Subread 10
flex 10
parallel 10
“pkg-config” 10
BEDOPS 9
DB 9
PCRE 9
PubWeb 9
“SciPy-bundle” 9
bsddb3 9
libpciaccess 9
libtool 9
texinfo 9
AlphaFold 8
cuDNN 8
itpp 8
kallisto 8
tbb 8
BamTools 7
“FASTX-Toolkit” 7
FriBidi 7
HarfBuzz 7
Homer 7
MEME 7
OpenMPI 7
PEAR 7
PLINK2 7
Pandoc 7
RSeQC 7
Trimmomatic 7
XZ 7
“beagle-lib” 7
git 7
seqtk 7
Apptainer 6
Bowtie 6
CUDA 6
EMBOSS 6
Emacs 6
HTSeq 6
IPython 6
Ruby 6
Trinity 6
minimap2 6
ArrayFire 5
CNVkit 5
GLib 5
GMP 5
IGVTools 5
“MAGeCK-VISPR” 5
MiXCR 5
PLINK 5
“RNA-SeQC” 5
bcl2fastq 5
cirro 5
fhCellRanger 5
texlive 5