Conda and Containers on LCC

Owned by UKY CCS RCD
yesterday at 10:00 am

The current list of conda packages and versions installed in the container are listed in the following table. To run the containers, see below:

Package name and versionEquivalent app name in the container to be used in the slurm scriptContainer Name and location
Notes
checkm-genome-1.1.2checkm112/share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf
deeptools-3.4.3deeptools343/share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf
ncl-6.6.2ncl662/share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf
ncview-2.1.7ncview217/share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf
quast-5.0.2quast502/share/singularity/images/ccs/conda/lcc-conda-ubuntu-20.04.sinf
roary-3.13.0roary3130/share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf
samtools-1.10samtools110/share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf
mummer4-4.0.0beta2mummer4400beta2/share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf
trinity-2.9.1trinity291/share/singularity/images/ccs/condls a/lcc-conda-1-centos8.sinf
wrf-python-1.3.2wrfpython132/share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf
blast-2.10.1blast2101/share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf
minimap2-2.17minimap2217/share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf
qiime2-2020.8.0qiime2202080/share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf
canu-2.1canu21/share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf
pilon-1.23pilon123/share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf
lastz-1.0.4lastz104/share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf
bayescan-2.0.1bayescan201/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
hyphy-2.5.17hyphy2517/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
macs-2.2.7.1macs2271/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
quorum-1.1.1quorum111/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
soapdenovo-2.40soapdenovo240/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
trinity2110trinity-2.11.0/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
fast5-0.6.5fast5065/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
fastx_toolkit-0.0.14fastx_toolkit0014/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
hisat2.2.1hisat221/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
htseq-0.12.4htseq0124/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
jellyfish-2.2.10jellyfish2210/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
jellyfish-2.2.6jellyfish226/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
mirdeep-2.0.1.2mirdeep2012/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
mrbayes-3.2.7mrbayes327/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
muscle-3.8.1551muscle381551/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
paml-4.9paml49/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
pcre-8.44pcre844/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
plink-1.90b6.12plink190b612/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
rnastructure-6.1rnastructure61/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
scons-3.1.2scons312/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
sra-tools-2.10.8sratools2108/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
stacks-2.53stacks253/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
star-2.7.5cstar275c/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
tophat-2.1.1tophat211/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
vcftools-0.1.16vcftools0116/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
velvet-1.2.10velvet1210/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinfsingularity run --app velvet1210 /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf velvetg
viennarna-2.4.15viennarna2415/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
fastqc-0.11.9fastqc0119/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
blast-2.10.1blast2101/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
bowtie-2.4.1bowtie241/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
bwa-0.7.17bwa0717/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
bedtools-2.29.2bedtools2292/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
cdhit-4.6.1cdhit461/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
mcl-14.137mcl14137/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
mafft-7.471mafft7471/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
guidance-2.0guidance202/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
raxml-8.2.12raxml8212/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
bismark-0.22.3bismark0223/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
gatk-4.1.8.1gatk4181/share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf
exonerate-gff3exonerategff3/share/singularity/images/ccs/conda/lcc-bio-1-centos8.sinf
implicit-landuseimplicitlanduse/share/singularity/images/ccs/conda/lcc-conda-4-centos8.sinf
gdal-3.1.2gdal312/share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf
bayescan-2.0.1bayescan201/share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf
bcftools-1.10.2bcftools1102/share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf
notebook-6.1.4 (includes pandas,numpy,scikit-learn)notebook614/share/singularity/images/ccs/conda/lcc-conda-4-centos8.sinf
mdanalysis-1.0.0mdanalysis/share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf
ensembl-vep-101.0ensemblvep1010/share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf
mothur-1.44.3mothur1443/share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf
mothur-1.44.11mothur14411/share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf
openbabel-2.4.1openbabel241/share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf
structure-2.3.4structure234/share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf
mega-10.1.8-1megax10181/share/singularity/images/ccs/MEGA/lcc-mega-10.1.8-1-centos8.sinf
bcftools-1.11 (includes samtools-1.11)
bcftools111/share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf
minigraphminigraph/share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf
annoy-1.17.0annoy1170/share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf
lammpss-deepmd-kit-module-gpulammpssdkmg/share/singularity/images/ccs/conda/lcc-conda-4-centos8.sinf
lammpss-deepmd-kit-module-cpulammpssdkmc/share/singularity/images/ccs/conda/lcc-conda-4-centos8.sinf
busco-5.0.0busco500/share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinfsingularity run --app busco500 /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf busco
SigProfilerExtractorSigProfilerExtractor/share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf
transdecoder-5.5.0transdecoder550 /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf
transrate-tools-1.0.0transratetools100/share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf
transrate-1.0.3transrate103/share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf
detonate-1.11detonate111/share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf
SPlisHSPlasHSPlisHSPlasH/share/singularity/images/ccs/splishsplash/SPlisHSPlasH.sinf
cd-hit-4.8.1cdhit481/share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf
cd-hit-auxtools-4.8.1cdhitauxtools481/share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf
dask-2021.2.0dask202120/share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf
dask-distributed-2021.2.0   daskdistributed202120/share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf
canu-2.1.1canu211/share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf
pb-assemblypbassembly/share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf
brakerbraker /share/singularity/images/ccs/braker/braker.sinf
blasr-5.3.5blasr535/share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf
megahit-1.2.9megahit129/share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf
trimmomatic-0.39trimmomatic039/share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf
mitozmitoz/share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf
methyldackel-0.5.2methyldackel052/share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf
qiime2-2021.2
qiime220212
/share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf
pbjellypbjelly/share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf
rnammer-1.2rnammer12/share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf
tmhmm-2.0ctmhmm20c/share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf
signalp-4.1signalP41/share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf
bioconductor-dss-2.38.0bioconductordss2380/share/singularity/images/ccs/conda/lcc-conda-R-1-centos8.sinf
r-peer-1.3rpeer13/share/singularity/images/ccs/conda/lcc-conda-R-conda-centos8.sinf
pytraj-2.0.4pytraj204/share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf
busco-5.1.2busco512/share/singularity/images/ccs/conda/lcc-conda-7-centos8.sinf
bowtie2-2.3.5-sra-linuxbowtie235sralinux/share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf
bowtie-2.4.2bowtie242/share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf
mdtraj-1.9.5mdtraj195/share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf
mothur-1.45.2mothur1452/share/singularity/images/ccs/conda/lcc-bio-1-centos8.sinf
breakdancer-1.4.5breakdancer145/share/singularity/images/ccs/conda/lcc-docker-break-dancer.sinf
lima-2.0.0lima200/share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf
bedops-2.4.39bedops2439/share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf
ambertools-20.15amber2015/share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf
tamatama  /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf
cdna_cupcake-22.0.0cdnacupcake2200/share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf
reindeerREINDEER/share/singularity/images/ccs/conda/lcc-conda-4-centos8.sinf
SQANTI3SQANTI3/share/singularity/images/ccs/conda/lcc-conda-4-centos8.sinf
mothur-1.45.3mothur1453/share/singularity/images/ccs/conda/lcc-bio-1-centos8.sinf
bismark-0.23.0bismark0230/share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf
hmmer-3.3.2hmmer332/share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf
humann-3.0.0.alpha.1humann300alpha1/share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf
velvet-1.2.10velvet1210/share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf singularity run --app velvet1210 /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf velvetg
pretext-suite-0.0.2pretextsuite002 /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf
tetools-1.4tetools14/share/singularity/images/ccs/tetools/tetools-1.4.sinf
trinityrnaseq-2.12.0trinityrnaseq2120/share/singularity/images/ccs/conda/trinityrnaseq-2.12.0.sinf
GFF3toolkit-2.0.3GFF3toolkit /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf
getorganelle-1.7.5.0getorganelle1750/share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf
mitobim-1.9.1mitobim/share/singularity/images/ccs/conda/MITObim.sinf
r-wgcna-1.69 rwgcna169 /share/singularity/images/ccs/conda/lcc-r-1-centos7-test.sinf
tpmcalculator-0.0.4tpmalculator004/share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf
novoplasty-4.2novoplasty42/share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf
mitofinder-1.4mitofinder14/share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf
velvetoptimiser-2.2.6velvetoptimiser226 /share/singularity/images/ccs/conda/./lcc-bio-1-centos7.sinfsingularity run --app velvetoptimiser226 /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf VelvetOptimiser.pl
jags-4.3.0jags430/share/singularity/images/ccs/conda/./lcc-bio-1-centos7.sinf
qiime2-2021.8qiime220218/share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf
perl-bioperl-1.7.2bioperl172/share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf
ancestry_hmmancestry_hmm/share/singularity/images/ccs/ancestry_HMM/armadillo-ancestry_hmm.sinf
MARTY1-3marty13/share/singularity/images/ccs/MARTY/1.3/marty-1.3.sinf
ngsToolsngsTools/share/singularity/images/ccs/ngsTools/ngsTools.sinfincludes bcftools-1.9, samtools-1.9, htslib-1.9 (from older versions combined)
spades-3.15.3spades3153/share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf
ngsutils-0.5.9ngsutils059/share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf
bcftools-1.13bcftools113 /share/singularity/images/ccs/ngsTools/samtools-1.13+matplotlib-bcftoools-1.13.sinf
samtools-1.13samtools113/share/singularity/images/ccs/ngsTools/samtools-1.13+matplotlib-bcftoools-1.13.sinf
angsd-0.910angsd0910/share/singularity/images/ccs/conda/lcc-conda-6-cento8.sinf
angsd-0.935angsd0935/share/singularity/images/ccs/conda/lcc-conda-6-cento8.sinf
ensembl-vep-104.3ensemblvep1043/share/singularity/images/ccs/conda/lcc-conda-6-cento8.sinf
angsd-0.931angsd0931/share/singularity/images/ccs/conda/lcc-conda-6-cento8.sinf
freebayes-1.3.4freebayes134/share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf
mashtree-1.2.0mashtree120/share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf
prokka1146prokka1146/share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf
angsd-0.933angsd0933/share/singularity/images/ccs/conda/lcc-conda-6-cento8.sinf
pybind11-2.8.0pybind11280/share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf
angsd-0.933angsd0933hstlib1110/share/singularity/images/ccs/conda/angsd_v0.933_hstlib_1.11.0.sinfangsd-0.933 with htslib: 1.11
mmseqs2-13.45111mmseqs21345111/share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf
svim-asm-1.0.2svimasm102/share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinfincludes minimap2 and samtools
pacbiopacbio/share/singularity/images/ccs/pacbio/pacbio.sinflima,pbccs,isoseq3
gtf2csvgtf2csv/share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinfsingularity run --app gtf2csv /share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf gtf2csv
phyml-3.3.20200621phyml3320200621/share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf
cactus-2.0.4
/share/singularity/images/ccs/cactus/cactus-2.0.4.sinfsee /share/examples/LCC/cactus
pbmm2-1.7.0pbmm2170/share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf
ragtag-2.1.0ragtag210/share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf
minimap2-2.24minimap2224/share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf
gmap-2021.08.25gmap20210825/share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinfsingularity run --app gmap20210825 /share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf gmap
sabre-1.000sabre1000/share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf singularity run --app sabre1000 /share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf sabre 
deepchem-2.5.0deepchem250/share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf singularity run --app deepchem250 /share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf python
adapterremoval-2.3.2adapterremoval232/share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinfsingularity run --app adapterremoval232 /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf AdapterRemoval
deepchem-2.6.1-GPUdeepchem261gpu/share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinfmodule load ccs/singularity
module load ccs/cuda/11.2.0_460.27.04
singularity run --app deepchem261gpu --nv /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf python
salmon-1.6.0salmon160/share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinfsingularity run --app salmon160 /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf salmon
opera-msoperams/share/singularity/images/ccs/opera-ms/opera-ms.sinfsingularity run --app operams /share/singularity/images/ccs/opera-ms/opera-ms.sinf
metaphlan-3.0.14metaphlan3014/share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinfsingularity run --app metaphlan3014 /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf metaphlan
biobakery_workflows-3.0.0a7biobakeryworkflows300a7/share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinfsingularity run --app biobakeryworkflows300a7 /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf biobakery_workflows_databases
humann2-2.8.1humann2281/share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinfsingularity run --app humann2281 /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf humann2
phylophlan302phylophlan302/share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinfsingularity run --app phylophlan302 /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf phylophlan
maaslin2-0.99.12maaslin209912/share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf*Invoke through R
kneaddata-0.10.0kneaddata0100/share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinfsingularity run --app kneaddata0100 /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf kneaddata
velocyto-0.17velocyto017/share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinfsingularity run --app velocyto017 /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf velocyto
mpdaf-3.5 and fitsio-1.1.7mpdaf35fitsio117/share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinfsingularity run --app mpdaf35fitsio117 /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf python
afterqc-0.9.7afterqc097 /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinfsingularity run --app afterqc097 /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf python /usr/local/Miniconda3/envs/afterqc-0.9.7/bin/after.py -1 R1.fq.gz
hmmer2gohmmer2go/share/singularity/images/ccs/hmmer2go/hmmer2go.sinfsingularity run --app hmmer2go /share/singularity/images/ccs/hmmer2go/hmmer2go.sinf hmmer2go
cgmaptoolscgmaptools/share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinfsingularity run --app cgmaptools /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf cgmaptools
cutadapt-3.7cutadapt37/share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinfsingularity run --app cutadapt37 /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf cutadapt
fastx_toolkit-0.0.14 fastxtoolkit00147/share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinfsingularity run --app fastxtoolkit00147 /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf fastq_to_fasta
finderFinder/share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinfsingularity run --app Finder /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf run_finder
DsuiteDsuite/share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinfsingularity run --app Dsuite /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf Dsuite
variantbam-1.4.4avariantbam144a/share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinfsingularity run --app variantbam144a /share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinf variant
qiskit-0.36.2qiskit0362/share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinf

singularity run --app qiskit0362 /share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinf python


cracklingcrackling/share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinfsingularity run --app crackling /share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinf Crackling -c config.ini (location of default config.ini in the container is /usr/local/Crackling/config.ini 
gist-pipelinegistpipeline/share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinfsingularity run --app gistpipeline /share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinf  gistPipeline
inotify-tools-3.20.2notifytools3202share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinf singularity run --app inotifytools3202 /share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinf inotifywatch
parallel-20220722parallel20220722share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinf singularity run --app parallel20220722 /share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinf parallel
NRI-MDNRIMD/share/singularity/images/ccs/conda/lcc-conda-4-rocky8.sinf

singularity run --app NRIMD /share/singularity/images/ccs/conda/lcc-conda-4-rocky8.sinf cp -R /usr/local/NRI-MD .

cd NRI-MD

singularity run --app NRIMD /share/singularity/images/ccs/conda/lcc-conda-4-rocky8.sinf python3 convert_dataset.py

MitoHiFi
/share/singularity/images/ccs/MitoHiFi/MitoHiFi.sinfsingularity exec /share/singularity/images/ccs/MitoHiFi/MitoHiFi.sinf findMitoReference.py
singularity exec /share/singularity/images/ccs/MitoHiFi/MitoHiFi.sinf mitohifi.py
agat-1.0.0agat100/share/singularity/images/ccs/conda/lcc-conda-5-rocky8.sinfsingularity run --app agat100 /share/singularity/images/ccs/conda/lcc-conda-5-rocky8.sinf agat
mothur-1.48.0mothur1480/share/singularity/images/ccs/conda/lcc-conda-5-rocky8.sinfsingularity run --app mothur1480 /share/singularity/images/ccs/conda/lcc-conda-5-rocky8.sinf mothur
clust-1.17.0clust1170share/singularity/images/ccs/conda/lcc-conda-6-rocky8.sinf singularity run --app clust1170 /share/singularity/images/ccs/conda/lcc-conda-6-rocky8.sinf clust
clust-1.8.10clust1810share/singularity/images/ccs/conda/lcc-conda-6-rocky8.sinf singularity run --app clust1810 /share/singularity/images/ccs/conda/lcc-conda-6-rocky8.sinf clust
snap-2013_11_29snap20131129/share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinfsingularity run --app snap20131129 /share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinf snap
kat-2.4.2kat242/share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinfsingularity run --app kat242 /share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinf kat
bowtie2-2.5.1bowtie2251/share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinfsingularity run --app bowtie2251 /share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinf bowtie2
busco-5.4.6busco546/share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinfsingularity run --app busco546 /share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinf busco
megan-6.24.20megan62420/share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinfsingularity run --app megan62420 /share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinf daa-meganizer
trim-galore-0.6.10trimgalore0610/share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinfsingularity run --app trimgalore0610 /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf trim_galore
bsbolt-1.4.8bsbolt148/share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinfsingularity run --app bsbolt148 /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf bsbolt
qiime2-amplicon-2023.9qiime2amplicon20239/share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinfsingularity run --app qiime2amplicon20239 /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf qiime
qiime2-shotgun-2023.9qiime2shotgun20239/share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinfsingularity run --app qiime2shotgun20239 /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf qiime
qiime2-tiny-2023.9qiime2tiny20239/share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinfsingularity run --app qiime2tiny20239 /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf qiime
deepvariant-1.6deepvariant/share/singularity/images/ccs/deepvariant/ccs-deepvariant-ubuntu2004.sifsingularity run -e --nv /share/singularity/images/ccs/deepvariant/ccs-deepvariant-ubuntu2004.sif /opt/deepvariant/bin/run_deepvariant
moose-2023-11-08moose/share/singularity/images/ccs/moose/ccs-moose-rocky8.sif

#Build MOOSE test app
singularity run -e /share/singularity/images/ccs/moose/ccs-moose-rocky8.sif bash -c 'make -j 24'

#Run MOOSE test app
singularity run -e /share/singularity/images/ccs/moose/ccs-moose-rocky8.sif bash -c './run_tests -j 24'

dorado-0.5.3doardo053/share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinfsingularity run --app dorado053 /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf dorado
pbtk-3.1.1 pbtk311/share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinfsingularity run --app pbtk311 /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf bam2fastq
minimap2-2.28minimap2228/share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinfsingularity run --app minimap2228 /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf minimap2
qiime2-amplicon-2024.2qiime2amplicon20242/share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinfsingularity run --app qiime2amplicon20242 /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf qiime
qiime2-shotgun-2024.2qiime2shotgun20242/share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinfsingularity run --app qiime2shotgun20242 /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf qiime
GLnexus-1.4.1-3glnexus1413/share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinfsingularity run --app glnexus1413 /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf glnexus_cli
fastp-0.23.4-3fastp02343/share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinfsingularity run --app fastp02343 /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf fastp
beast2-2.6.3-2 (with beagle-lib 4.0.0)beast22632/share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinfsingularity run --app beast22632 /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf beast -beagle_info
Dsuite-0.5-r57Dsuite05r57/share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf 

singularity run --app Dsuite05r57 /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf Dsuite -h

Angsd v0.940angsd0940 /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf singularity run --app angsd0940 /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf angsd --help
PartitionFinder v2.1.1PartitionFinder211/share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf singularity run --app PartitionFinder211 /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf python /usr/local/Miniconda3/envs/PartitionFinder-211/partitionfinder-2.1.1/PartitionFinder.py -h
phyml v3.3.20220408

phyml3320220408

/share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf 

singularity run --app phyml3320220408 /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf phyml -h

ngsDist v1.0.10ngsdist1010/share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf 

singularity run --app ngsdist1010 /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf /usr/local/ngsDist/ngsDist

ciao v4.16ciao416/share/singularity/images/ccs/ciao/ciao-416.sinfsingularity run --app ciao416 /share/singularity/images/ccs/ciao/ciao-416.sinf ciaover -v
PyTorch 2.3.0 / CUDA 12.4
/share/singularity/images/ccs/pytorch/pytorch-24.04-py3.sinfsingularity exec --nv /share/singularity/images/ccs/pytorch/pytorch-24.04-py3.sinf python
PyTorch 2.2.0 / CUDA 12.3.2
/share/singularity/images/ccs/pytorch/pytorch-24.01-py3.sinfsingularity exec --nv /share/singularity/images/ccs/pytorch/pytorch-24.01-py3.sinf python
Tassel v5.2.89tassel5289/share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinfsingularity run --app tassel5289 /share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinf start_tassel.pl -Xmx4g
GBS-SNP-CROP v4.1 gbssnpcrop41/share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinfsingularity run --app gbssnpcrop41 /share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinf perl /usr/local/GBS-SNP-CROP-v.4.1/GBS-SNP-CROP-scripts/v.4.1/GBS-SNP-CROP-1.pl
samtools 1.20samtools120/share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinfsingularity run --app samtools120 /share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinf samtools 

Can also execute with "samtools-1.20 samtools"
bcftools 1.20bcftools120/share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinfsingularity run --app bcftools120 /share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinf bcftools 

Can also execute with "bcftools-1.20 bcftools"
beast2-2.7.7 (with beagle-lib 4.0.1)beast2277/share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinf

singularity run --app beast2277 /share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinf beast

singularity run --app beast2277 /share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinf packagemanager

lightning v2.3.1(with timm v1.0.7 and python-dotenv1.01)
/share/singularity/images/ccs/pytorch/pytorch-24.04-py3.sinfsingularity exec --nv /share/singularity/images/ccs/pytorch/pytorch-24.04-py3.sinf python -c "import sys, torch, lightning as L, timm, pkg_resources; print(f'Python version: {sys.version}'); print(f'PyTorch version: {torch.__version__}'); print(f'Lightning version: {L.__version__}'); print(f'timm version: {timm.__version__}'); print(f'python-dotenv version: {pkg_resources.get_distribution(\"python-dotenv\").version}')"
R-plm_1.65rplm165/share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinfmodule load ccs/singularity-3.8.2
singularity run --app rplm165 /share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinf R
CmdStanR 0.5.2 and OpenCL
/share/singularity/images/ccs/cmdstanr/lcc-cmdstanr-opencl.sinfsingularity exec --overlay=$OVERLAY --nv /share/singularity/images/ccs/cmdstanr/lcc-cmdstanr-opencl.sinf Rscript example.R
nginx-1.25.3nginx1253/share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinf

module load ccs/singularity-3.8.2

singularity run --app nginx1253 /share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinf nginx

ird-2.0.4.2idr202/share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinf

module load ccs/singularity-3.8.2

singularity run --app idr2042 /share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinf idr --help

Dsuite-0.5-r58Dsuite05r58/share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinf

singularity run --app Dsuite05r58 /share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinf Dsuite -h

feems v1.0.1feems101/share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinfsingularity run --app feems101 /share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinf python
delly v1.3.1delly131/share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinfsingularity run --app delly131 /share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinf delly --help
gridss v2.13.2gridss2132/share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinfsingularity run --app gridss2132 /share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinf gridss
sniffles v2.5.3-0sniffles2530/share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinfsingularity run --app sniffles2530 /share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinf sniffles --help


How to Run Containerized Programs

There are two ways to run containerized programs: 1) Interactively, or 2) Via a SLURM  job submission script. The first method provides a way to check the environment and testing program configuration/options, but is not meant for a full production run as it will take up resources in the login nodes. When you are ready to run the job in the compute nodes, you can do method #2 below.  

 1) To run a software package installed in the conda container interactively:

1. Load singularity module   

[user@login001]$ module load ccs/singularity

2. Invoke the singularity container shell.

[user@login001]$ singularity shell /share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf 

3. Activate the conda environment for whichever package you want to use, eg samtools-1.10 (the conda package name to be used for interactive use is from column 1 from the above table)

Singularity lcc-conda-1-centos8.sinf :~> . activate samtools-1.10

4. Then use the package as intended

(samtools-1.10) Singularity lcc-conda-1-centos8.sinf :~> samtools --version
samtools 1.10
Using htslib 1.10.2
Copyright (C) 2019 Genome Research Ltd.

5. After usage of that conda package

(samtools-1.10) Singularity lcc-conda-1-centos8.sinf :~> conda deactivate

6. Exit the singularity container

Singularity lcc-conda-1-centos8.sinf :~> exit

 2) To run a software package installed in the conda container in a SLURM job submission script.:

For eg. samtools-1.10 (The app name to be used for conda package is from the table above (column 2))

#!/bin/bash

#SBATCH -t 00:05:00                                                                                #Time for the job to run
#SBATCH --job-name=Conda-example                                                 #Name of the job

#SBATCH -n 1                                                                                           #Number of cores needed for the job; cannot be more than the number of cores available on a single node
#SBATCH --partition=CAS48M192_D                                                     #Name of the queue

#SBATCH --mail-type ALL                                                                       #Send email on start/end
#SBATCH --mail-user xxxxxx@uky.edu                                                 #Where to send email

#SBATCH --account=col_XXXXX_uksr                                                    #Name of slurm account to run under

#Module needed to run the conda job
module load ccs/singularity

echo "Job $SLURM_JOB_ID running on SLURM NODELIST: $SLURM_NODELIST "

#Samtools program execution command

singularity run --app samtools110   /share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf   samtools --version 

This example is available in the folder  /share/examples/LCC/conda


Center for Computational Sciences