Installed Software

CRC uses the lmod environment modules system to provision software to our users. To query whether a software is available, use

module spider <name_of_software>

Listed below are all the installed software as of 08/2022 on our system:

 

3seq

abaqus

abinit

abinit-epg

abyss

adf

admixmap

admixture

advisor

af4

afni

albacore

amber

amd

ancestrymap

anndata

annovar

ansys

ansysem

ants

arboreto

arcashla

aria2

arpack

arriba

aspeak

atacseq_harvard

ataqv

athlates

augustus

autodock_vina

awscli

azcopy

bamqc

bam-readcount

bamtools

bamutil

basespace

bash

bats

bazel

bbmap

bcbio-nextgen

bcftools

bcl2fastq2

beast

bedops

bedtools

berkeleygw

bioawk

biobambam2

bionano

bionano_tools

biopython

biotoolbox

bismark

bison

blast+

blender

bonito

boost

boost-compiled

bowtie

bowtie2

braker2

breseq

busco

bustools

bwa

bwa-mem2

bwtool

byobu

bzip2

cactus

cadence

cadical

caffe

calibre

cantera

canu

cap3

caper

causalml

cellphonedb

cellranger

cellranger-arc

cellranger-atac

cellxgene

chapel

checkm

chroma

chrome

chromedriver

circompara

circos

ciscall

cite-seq-count

clang

clark

clc-assembly-cell

clinker

clinqc

clonalframeml

cmake

cmappy

cnvkit

cnvnator

code-server

comsol

conn_toolbox

control-freec

convert3d

cooler

cosmosscope

cp2k

cpat

crimap

cromwell

ctpnet

cuba

cuda

cufflinks

curl

custom_waveview

customsim

cutadapt

cutruntools

cytoscape

damask

danpos2

dapars

datalad

dcm2niix

deepbinner

deeplabcut

deeptools

deepvariant

defuse

degnorm

delly

detonate

deviceQuery

diachromatic

diamond

discovardenovo

dms_tools2

doxygen

drop-seq

dsistudio

dx-toolkit

dynare

eagle

eclipidrmergepeaks

edirect

eigen

eman2

emboss

emmax

encfs

epacts

expat

fabtests

fanc

fastp

fastq_pair

fastq_screen

fastqc

fasttree

fastx-toolkit

fdtd

febio

ffmpeg

fftw

fhiaims

finesim

fish

fitsio

flashpca

flex

flye

fontconfig

fqtrim

freebayes

freefem

freesurfer

f-seq

fsl

fsleyes

fsps

fusioncatcher

fusion-inspector

gamess

gatb

gatk

gaussian

gblocks

gcc

gdal

gdc-tsv-tool

gdma

gdrcopy

genotypeharmonizer

genrich

geos

gfold

ghostscript

gistic

git

git-annex

github

glew

glimmer

glnexus

glpk

gmap-gsnap

gmsh

gnuplot

go

gomcl

google-cloud-sdk

googletest

gossamer

gotcloud

gpaw

gperf

grace

graphviz

gromacs

gsl

gubbins

gulp

guppy

gurobi

gym

hail

hclust

hdf5

hifive

hisat2

hmmer

homer

hpl

hspice

htseq

htslib

humann2

hydra

hypre

icount

idp

idp-fusion

idr

igv

imagej

imagemagick

indrops

infercnv

inspector

intel

intel-mpi

ipc

ipyrad

itk

iva

jaaba

jags

jansson

java

jbrowse2

jdftx

jellyfish

jmol

joe

julia

kaldi

kallisto

kentutils

kite

kneaddata

kpp

kraken2

krona

lammps

lapack

lc

lcov

ldpred

leafcutter

libevent

libfabric

libfaketime

libgtextutils

libjpeg

libpng

libtiff

libxc

libxml2

libzmq

lightgbm

lncfuntk

lofreq

lohhla

loompy

loomr

lua

luarocks

lumerical

macs

mafft

magicblast

magma

make

malt

manta

mapsplice2

masurca

mathematica

matlab

matlab-mcr

matlab-proxy

mauve

maven

medea

meerkat

mega2

megahit

megalodon

meme

merlin

meshlab

metabat2

metal

metaphlan

metis

mgltools

midnightcommander

minimac4

mira

mirdeep2

mirge

miso

mixcr

mkl

mmseqs2

modeller

modelsim

molden

molecularGSM

molpro

mongodb

mopac

mosek

mpich

mricrogl

mricron

mrtrix

mrtrix3

multinest

multiqc

mummer

muscle

mutsig

namd

nano

nanoplot

nauty

nccl

nektar

nektar++

neovim

netcdf

netpbm

neuron

nextflow

nextgenmap

nfcore

nf-core

ngmerge

ngsplot

ngsqc

nodejs

novocraft

nucleoatac

nvshmem

onedrive

openbabel

openblas

open-cravat

opencv

openfoam

openmolcas

openmpi

openslide-python

optitype

orca

osss-ucx

ovito

p7zip

packmol

paml

pandoc

pangolin

parallel

paraview

parmetis

parsplice

pathml

pcre

pda

peakdeck

peakseq

peaksplitter

pear

pedcheck

perl

petsc

petsc-gcc

pgi

phast

php

phylip

phyloacc

phyx

picard

pigz

pilon

pindel

piranha

pizzly

plink

plinkseq

plotjuggler

plumed

pmix

poltype

poppler

popt

porechop

postgresql

povray

primer3

prinseq

proj

prokka

proovread

provirus

psi4

pureclip

pvactools

pybedtools

pycharm

pychopper

pyrouge

pyscenic

python

pytorch

pytorch_gpu

qapa

qchem

qiime2

qorts

qt

qualimap

quantumespresso

quast

quickmirseq

r

racon

radia

rapsearch

raxml-ng

rclone

rdkit

readtools

reforge

regina

regtools

relion

rgt

rmats

rnachipintegrator

rnacocktail

rna-seqc

rnaseqmut

rosetta

rsem

rseqc

rstudio

rtg-core

s4

salmon

sambamba

samblaster

samstat

samtools

sas

scala

scanpy

scats

scbayes

seqcover

seqkit

seqspark

seqtk

shap

shapeit4

sicer

sickle

siesta

simpleitk

singularity

slurm

smoove

snakemake

snap-aligner

snpeff

snp-pileup

snptest

snver

snvmix2

soapindel

solar

somatic-sniper

sortmerna

sox

spaceranger

spades

spark

sparrow

spladder

spm

spreg

squashfs-tools

squid

sra-toolkit

srnanalyzer

star

star-fusion

star-seqr

stata

strelka

stringtie

structure

stubb

subread

surfaceGSM

svaba

svdetect

svviz2

synopsys

taiji

taiji-view

teaching

telescope

tensorflow

texlive

tinker

tmux

tokyo

tophat

torch

tpmcalculator

tracer

transdecoder

trf

trilinos

trimgalore

trimmomatic

trinity

trust

trust4

turbomole

ucsc-cell-browser

ucx

uintah

ultimaker-cura

umi-tools

unceqr

valgrind

vardictjava

varscan

vasp

vasp-vtst

vcf2maf

vcflib

vcftools

vcs

vdjtools

velocyto

velvet

venv

vep

vfs

vim

virtualgl

virtuoso-opensource

virus_detection_sra

virusfinder

virvarseq

visit

vlsi

vmd

vscode

vtk

vtune

vvp

westpa

wine

xhmm

xilinx/containers

xilinx/sdx

xilinx/vitis

xilinx/vivado

xtb

xz

zlib

zoltan