Software list for singularity containers for conda packages in the MCC cluster

Owned by UKY CCS RCD
Dec 10, 2024

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 version   

Equivalent app in the container to be used in the SLURM script                          

Container name and location                              

Notes

tk-8.6.10

tk8610

/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf


cellranger-6.1.1

cellranger611

/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf


spaceranger-1.3.0

spaceranger130

/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf


sra-tools-2.11.0

sratools2110

/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf


pymatgen-2022.0.12

pymatgen2022012

/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf

pymatgen+ocelot+rdkit

minimap-2.22

minimap222

/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf


autodock_vina_1_1_2

vina112

/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf


purge_dups-1.2.5

purgedups125

/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf


breakdancer1.4.5

breakdancer145

/share/singularity/images/ccs/conda/mcc-docker-break-dancer.sinf


blast-2.12.0

blast2120

/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf


plink-1.90b6.21

plink190b621

/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf


mirdeep2-2.0.1.2

mirdeep22012

/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf


r-seurat-4.0.4

rseurat404

/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf


bwa-0.7.17

bwa0717

/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf


cellranger-3.1.0

cellranger310

/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf


hifiasm-0.16.1

hifiasm0161

/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf


pbmm2-1.7.0

pbmm2170

/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf


salsa2-2.3

salsa223

/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf

singularity run --app salsa223 /share/singularity/images/ccs/conda/amd-conda1-centos8.sinf python /usr/local/Miniconda3/envs/salsa2-2.3/bin/run_pipeline.py

deepvariant-1.2.0


/share/singularity/images/ccs/deepvarient/ccs-deepvariant-1.2.0.sinf

See /share/examples/MCC/deepvariant

bcftools-1.13

bcftools113

/share/singularity/images/ccs/ngstools/samtools-1.13+matplotlib-bcftoools-1.13.sinf

singularity run --app samtools113 /share/singularity/images/ccs/ngstools/samtools-1.13+matplotlib-bcftoools-1.13.sinf bcftools

samtools-1.13

samtools113

/share/singularity/images/ccs/ngstools/samtools-1.13+matplotlib-bcftoools-1.13.sinf

singularity run --app samtools113 /share/singularity/images/ccs/ngstools/samtools-1.13+matplotlib-bcftoools-1.13.sinf samtools

gatk4-4.2.2.0

gatk44220

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


ngsTools

ngsTools

/share/singularity/images/ccs/ngsTools/ngsTools.sinf

includes bcftools-1.9, samtools-1.9, htslib-1.9 (from older versions combined)

angsd-0.910

angsd0910

/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf


angsd-0.931

angsd0931

/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf


angsd-0.935

angsd0935

/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf


angsd-0.933

angsd0933

/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf


angsd-0.933 

angsd0933hstlib1110

/share/singularity/images/ccs/conda/angsd_v0.933_hstlib_1.11.0.sinf

angsd-0.933 with htslib: 1.11

cortex_con-0.04c

cortexcon004c

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


ambertools-21.10

ambertools2110

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


autodock-vina-1.1.2

aautodockvina112

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


pytraj-2.0.5

pytraj205

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


beagle-5.2_21Apr21.304

beagle5221Apr21304

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


vcftools-0.1.16

vcftools0116

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


gatk4-4.2.2.0

gatk44220

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


picard-2.26.4

picard2264

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf

singularity run --app picard2264 /share/singularity/images/ccs/conda/amd-conda2-centos8.sinf java -jar /usr/local/picard-2.26.4/picard.jar -h

hifiasm-0.16.1

hifiasm0161

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


bedtools-2.30.0

bedtools2300

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


cufflinks-2.2.1

cufflinks221

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


mothur-1.46.1

mothur1461

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


kraken2-2.1.2

kraken2212

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf

singularity run --app kraken2212 /share/singularity/images/ccs/conda/amd-conda2-centos8.sinf kraken2-build --standard --threads 24 --db plant

inspector

inspector

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf

singularity run --app inspector /share/singularity/images/ccs/conda/amd-conda2-centos8.sinf inspector.py

rsem

rsem

/share/singularity/images/ccs/conda/mcc-rsem-docker-ubuntu.sinf

singularity exec /share/singularity/images/ccs/conda/mcc-rsem-docker-ubuntu.sinf 

freebayes1.3.5

freebayes135

/share/singularity/images/ccs/conda/amd-conda4-centos8.sinf 


star-2.7.9a

star279a

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


ragtag-2.1.0

ragtag210

/share/singularity/images/ccs/conda/amd-conda4-centos8.sinf


SDA

SDA

/share/singularity/images/ccs/conda/amd-conda4-centos8.sinf 


bowtie2-2.4.4

bowtie2244

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


hisat2-2.2.1

hisat2221

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


velvet-1.2.10

velvet1210

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


perl-velvetoptimiser-2.2.6

perlvelvetoptimiser226

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


trimmomatic-0.39

trimmomatic039

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


structure-2.3.4

structure234

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


beast-1.10.4

beast1104

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


beast2-2.6.3

beast2263

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


mrbayes-3.2.7

mrbayes327

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


raxml-8.2.12

raxml8212

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf

singularity run --app raxml8212 /share/singularity/images/ccs/conda/amd-conda2-centos8.sinf raxmlHPC-AVX2 -h (SERIAL)

singularity run --app raxml8212 /share/singularity/images/ccs/conda/amd-conda2-centos8.sinf raxmlHPC-PTHREADS-AVX2 -h (THREADED)

muscle-3.8.1551

muscle381551

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


ont-guppy-cpu_3.0.3

ontguppycpu303

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


stringtie-2.1.7

stringtie217

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


astral-5.7.3

astral573

/share/singularity/images/ccs/conda/amd-conda2-centos8.sinf


bowtie2-2.4.4

bowtie2244

/share/singularity/images/ccs/conda/amd-conda4-centos8.sinf


bowtie2-2.3.5-sra-linux

bowtie235sralinux

/share/singularity/images/ccs/conda/amd-conda4-centos8.sinf


blasr-5.3.5

blasr535

/share/singularity/images/ccs/conda/amd-conda4-centos8.sinf


pbjelly

pbjelly

/share/singularity/images/ccs/conda/amd-conda4-centos8.sinf


pretext-suite-0.0.2

pretextsuite002

/share/singularity/images/ccs/conda/amd-conda4-centos8.sinf


trinity-2.13.2

trinity2132

/share/singularity/images/ccs/conda/amd-conda4-centos8.sinf


tetools-1.4

tetools14

/share/singularity/images/ccs/tetools/tetools-1.4.sinf

See details here https://github.com/Dfam-consortium/TETools to run the container

biopython-1.79

biopython179

/share/singularity/images/ccs/conda/amd-conda4-centos8.sinf

singularity run --app biopython179 /share/singularity/images/ccs/conda/amd-conda4-centos8.sinf python

snakemake-6.12.3

snakemake6123

/share/singularity/images/ccs/conda/amd-conda4-centos8.sinf

singularity run --app snakemake6123 /share/singularity/images/ccs/conda/amd-conda4-centos8.sinf snakemake

biopython, bioperl, bowtie2, bwa-mem, star, hisat2, tophat, cufflinks, stringtie, samtools, GATK, picard, vcftools and bcftools

pipeline1

/share/singularity/images/ccs/conda/amd-pipeline1-centos8.sinf

Pipeline to run multiple packages from a single container

singularity run --app pipeline1 /share/singularity/images/ccs/conda/amd-pipeline1-centos8.sinf

RepeatMasker-4.1.2-p1

RepeatMasker

/share/singularity/images/ccs/tetools/tetools-1.4.sinf

singularity run --app tetools14 /share/singularity/images/ccs/tetools/tetools-1.4.sinf RepeatMasker

To customize RepeatMasker Libraries see  https://github.com/Dfam-consortium/TETools#customizing-the-repeatmasker-libraries 

samtools-1.15-libdeflate

samtools115

/share/singularity/images/ccs/samtools-libdeflate/samtools-1.15.sinf

singularity run --app samtools115 /share/singularity/images/ccs/samtools-libdeflate/samtools-1.15.sinf samtools

ngsLD

ngsLD 

/share/singularity/images/ccs/ngsLD/ngsLD.sinf 

singularity run --app ngsLD /share/singularity/images/ccs/ngsLD/ngsLD.sinf ngsLD

singularity run --app ngsLD /share/singularity/images/ccs/ngsLD/ngsLD.sinf perl /usr/local/ngsLD/scripts/prune_graph.pl

singularity run --app ngsLD /share/singularity/images/ccs/ngsLD/ngsLD.sinf Rscript /usr/local/ngsLD/scripts/fit_LDdecay.R

qiime2-2022.2

qiime220222

/share/singularity/images/ccs/conda/amd-conda1-rocky8.sinf

singularity run --app qiime220222 /share/singularity/images/ccs/conda/amd-conda1-rocky8.sinf qiime

verifybamid2

verifybamid

/share/singularity/images/ccs/verifybamid2/verifybamid2.sinf

singularity run --app verifybamid /share/singularity/images/ccs/verifybamid2/verifybamid2.sinf VerifyBamID

masurca-4.0.8

masurca408

/share/singularity/images/ccs/conda/amd-conda3-rocky8.sinf

singularity run --app masurca408 /share/singularity/images/ccs/conda/amd-conda3-rocky8.sinf masurca

hypo-1.0.3

hypo103

/share/singularity/images/ccs/conda/amd-conda3-rocky8.sinf

singularity run --app hypo103 /share/singularity/images/ccs/conda/amd-conda3-rocky8.sinf hypo

busco-5.3.0

busco530

/share/singularity/images/ccs/conda/amd-conda3-rocky8.sinf

singularity run --app busco530 /share/singularity/images/ccs/conda/amd-conda3-rocky8.sinf busco

talon-5.0

talon50

/share/singularity/images/ccs/conda/amd-conda2-rocky8.sinf

singularity run --app talon50 /share/singularity/images/ccs/conda/amd-conda2-rocky8.sinf talon

SQANTI3

SQANTI3

/share/singularity/images/ccs/conda/amd-conda2-rocky8.sinf

singularity run --app SQANTI3 /share/singularity/images/ccs/conda/amd-conda2-rocky8.sinf python /usr/local/SQANTI3-4.2/sqanti3_qc.py

singularity run --app SQANTI3 /share/singularity/images/ccs/conda/amd-conda2-rocky8.sinf python /usr/local/SQANTI3-4.2/sqanti3_RulesFilter.py

tama

tama

/share/singularity/images/ccs/conda/amd-conda2-rocky8.sinf

singularity run --app tama /share/singularity/images/ccs/conda/amd-conda2-rocky8.sinf python /usr/local/tama/tama_collapse.py

singularity run --app tama /share/singularity/images/ccs/conda/amd-conda2-rocky8.sinf python /usr/local/tama/tama_merge.py

opera-ms

operams

/share/singularity/images/ccs/opera-ms/opera-ms.sinf


singularity run --app operams /share/singularity/images/ccs/opera-ms/opera-ms.sinf

cdna_cupcake-28.0.0

cdna_cupcake2800

/share/singularity/images/ccs/conda/amd-conda2-rocky8.sinf

singularity run --app cdna_cupcake2800 /share/singularity/images/ccs/conda/amd-conda2-rocky8.sinf

cogent 

cogent

/share/singularity/images/ccs/conda/amd-conda2-rocky8.sinf

singularity run --app cogent /share/singularity/images/ccs/conda/amd-conda2-rocky8.sinf run_mash.py

pcangsd-0.98.2

pcangsd0982

/share/singularity/images/ccs/conda/amd-conda4-rocky8.sinf

singularity run --app pcangsd0982 /share/singularity/images/ccs/conda/amd-conda4-rocky8.sinf pcangsd

iqtree-2.2.0_beta

iqtree220beta

/share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf

singularity run --app iqtree220beta /share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf  iqtree

bwakit-0.7.17.dev1

bwakit0717dev1

/share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf

singularity run --app bwakit0717dev1 /share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf bwa

samblaster-0.1.26

samblaster0126

/share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf

singularity run --app samblaster0126 /share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf samblaster

sambamba-0.8.2

sambamba082

/share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf

singularity run --app sambamba082 /share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf sambamba

methyldackel-0.6.1

methyldackel061

/share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf

singularity run --app methyldackel061 /share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf MethylDackel

bwameth-0.2.4

bwameth024

/share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf

singularity run --app bwameth024 /share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf bwameth.py

bismark-0.23.1

bismark0231

/share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf

singularity run --app bismark0231 /share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf bismark_genome_preparation

openbabel-3.1.1

openbabel311

/share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf

singularity run --app openbabel311 /share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf obabel

hisat2-2.1.0

hisat2210

/share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf

singularity run --app hisat2210 /share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf hisat2

laser-2.04

laser204

/share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf

singularity run --app laser204 /share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf laser

bedops-2.4.39

bedops2439

/share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf

singularity run --app bedops2439 /share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf  vcf2bed

Azure azcopy-10.15.0

azcopy10150

/share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf

singularity run --app azcopy10150 /share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf  azcopy

kallisto-0.48.0

kallisto0480

/share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf

singularity run --app kallisto0480 /share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf  kallisto

cellranger-7.0.0

cellranger700

/share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf

singularity run --app cellranger700 /share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf cellranger

rcorrector-1.0.4

rcorrector104

/share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf

singularity run --app rcorrector104 /share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf rcorrector

r-seurat-4.1.1

rseurat411

/share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf

singularity run --app rseurat411 /share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf R

singularity run --app rseurat411 /share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf Rscript

orthofinder-2.5.4

orthofinder254

/share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf

singularity run --app orthofinder254 /share/singularity/images/ccs/conda/amd-conda5-rocky8.sinf orthofinder

mcclintock

mcclintock



blat-36

blat36

/share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf

singularity run --app blat36 /share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf blat

HTSeq-2.0.2

HTSeq202

/share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf

singularity run --app HTSeq202 /share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf htseq-count 

gffcompare

gffcompare

/share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf

singularity run --app gffcompare /share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf gffcompare

singularity run --app gffcompare /share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf trmap

merqury-1.3

merqury13

/share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf

singularity run --app merqury13 /share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf merqury.sh

fastqc-0.11.3

fastqc0113

/share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf

singularity run --app fastqc0113 /share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf fastqc

trim-galore-0.4.3

trimgalore043

/share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf

singularity run --app trimgalore043 /share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf trim_galore

fastqc-0.11.9

fastqc0119

/share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf

singularity run --app fastqc0119 /share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf fastqc

r-seurat-4.0.4+MAST+

DESeq2

rseurat404

/share/singularity/images/ccs/users/irci222/amd-rseurat.sinf

singularity run --app rseurat404 /share/singularity/images/ccs/users/irci222/amd-rseurat.sinf R

r-seurat-4.1.1+MAST+

DESeq2

rseurat411

/share/singularity/images/ccs/users/irci222/amd-rseurat.sinf

singularity run --app rseurat411 /share/singularity/images/ccs/users/irci222/amd-rseurat.sinf R

qiskit-0.36.2

qiskit0362

/share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf 

singularity run --app qiskit0362 /share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf  python

cellranger-atac-2.1.0

cellrangeratac210

/share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf 

singularity run --app cellrangeratac210 /share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf cellranger-atac

reditools2

reditools2

/share/singularity/images/ccs/reditools2/reditools2-conda.sinf

singularity run --app reditools2 /share/singularity/images/ccs/reditools2/reditools2-conda.sinf prepare_test.sh

singularity run --app reditools2 /share/singularity/images/ccs/reditools2/reditools2-conda.sinf python /usr/local/reditools2.0/src/cineca/reditools.py -f /usr/local/reditools2.0/test/SRR2135332.bam -r chr21.fa -g chr21 -o serial_table.txt

reditools1


/share/singularity/images/ccs/reditools2/reditools1.sinf

singularity exec /share/singularity/images/ccs/reditools2/reditools1.sinf python /REDItools/main/REDItoolDenovo.py
singularity exec /share/singularity/images/ccs/reditools2/reditools1.sinf python /REDItools/main/REDItoolDnaRna.py
singularity exec /share/singularity/images/ccs/reditools2/reditools1.sinf python /REDItools/main/REDItoolKnown.py

mcclintock

mcclintock

/share/singularity/images/ccs/conda/amd-conda7-rocky8.sinf

singularity run --app mcclintock /share/singularity/images/ccs/conda/amd-conda7-rocky8.sinf python3 /usr/local/mcclintock/mcclintock.py -r /usr/local/mcclintock/test/sacCer2.fasta -c /usr/local/mcclintock/test/sac_cer_TE_seqs.fasta -g /usr/local/mcclintock/test/reference_TE_locations.gff -t /usr/local/mcclintock/test/sac_cer_te_families.tsv -1 /usr/local/mcclintock/test/SRR800842_1.fastq.gz -2 /usr/local/mcclintock/test/SRR800842_2.fastq.gz -p 4 -o test

tpmcalculator-0.0.4

tpmcalculator004

/share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf

singularity run --app tpmcalculator004 /share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf TPMCalculator

seqtk-1.3

seqtk13

/share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf

singularity run --app seqtk13 /share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf seqtk

diamond-2.0.15

diamond2015

singularity run --app diamond2015 /share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf diamond

singularity run --app diamond2015 /share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf diamond

salmon-1.9.0

salmon190

/share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf

singularity run --app salmon190 /share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf salmon

crackling

crackling

/share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf

singularity run --app crackling /share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf Crackling -c config.ini (location of default config.ini in the container is /usr/local/Crackling/config.ini 



/share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinf

singularity run --app crackling /share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinf Crackling

macs2 2.2.7.1

macs22271

/share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf

singularity run --app macs22271 /share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf macs2

clust-1.17.0

clust1170

/share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf

singularity run --app clust1170 /share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf clust

inotify-tools-3.20.2

notifytools3202

/share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf

singularity run --app inotifytools3202 /share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf inotifywatch

parallel-20220722

parallel20220722

/share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf

singularity run --app parallel20220722 /share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf parallel

argweaver-20200306

argweaver20200306

/share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf

singularity run --app argweaver20200306 /share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf arg-sample

bcftools + plugins


/share/singularity/images/ccs/conda/amd-pipeline1-centos8.sinf

singularity run --app pipeline1 /share/singularity/images/ccs/conda/amd-pipeline1-centos8.sinf bcftools plugin --list-plugins

singularity run --app pipeline1 /share/singularity/images/ccs/conda/amd-pipeline1-centos8.sinf bcftools +fill-tags -l

perl-bio-viennangs-0.19.2

perlbioviennangs0192

/share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf

singularity run --app perlbioviennangs0192 /share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf bed2bedGraph.pl -h

ucsc-bedgraphtobigwig-377

ucscbedgraphtobigwig377

/share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf

singularity run --app ucscbedgraphtobigwig377 /share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf bedGraphToBigWig

homer-4.11

homer411

/share/singularity/images/ccs/conda/amd-conda8-rocky8.sinfamd-conda13-rocky8.defc

singularity run --app homer411 /share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf homer2

psi4-1.6.1+5b9f6e3

psi41615b9f6e3

/share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf

singularity run --app psi41615b9f6e3 /share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf psi4

agptools

agptools

/share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf

singularity run --app agptools /share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf agptools 

deeptools-3.5.1

deeptools351

/share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf

singularity run --app deeptools351 /share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf deeptools

plink2-2.00a3.3

plink2200a33

/share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf

singularity run --app plink2200a33 /share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf plink2

gtf2csv 

gtf2csv 

/share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf

singularity run --app gtf2csv /share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf gtf2csv

jellyfish-2.2.10

jellyfish2210

/share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf

singularity run --app jellyfish2210 /share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf jellyfish

medaka-1.7.2

medaka172

/share/singularity/images/ccs/conda/amd-conda9-rocky8.sinf

singularity run --app medaka172 /share/singularity/images/ccs/conda/amd-conda9-rocky8.sinf medaka

flye-2.9.1

flye291

/share/singularity/images/ccs/conda/amd-conda9-rocky8.sinf

singularity run --app flye291 /share/singularity/images/ccs/conda/amd-conda9-rocky8.sinf flye

cellranger-arc-2.0.2

cellrangerarc202

/share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf

singularity run --app cellrangerarc202 /share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf cellranger-arc

REINDEER

reindeer

/share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf

singularity run --app reindeer /share/singularity/images/ccs/conda/amd-conda6-rocky8.sinf Reindeer

salsa2-2.3

salsa223

/share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf 

singularity run --app salsa223 /share/singularity/images/ccs/conda/amd-conda8-rocky8.sinf python /usr/local/Miniconda3/envs/salsa2-2.3/bin/run_pipeline.py

popoolation2_1201

Popoolation2

/share/singularity/images/ccs/Popoolation/Popoolation.sinf

singularity run --app Popoolation2 /share/singularity/images/ccs/Popoolation/Popoolation.sinf perl /usr/local/popoolation2_1201/snp-frequency-diff.pl --test

popoolation_1.2.2

Popoolation

/share/singularity/images/ccs/Popoolation/Popoolation.sinf

singularity run --app Popoolation /share/singularity/images/ccs/Popoolation/Popoolation.sinf perl /usr/local/popoolation_1.2.2/basic-pipeline/trim-fastq.pl --help

spades-3.15.5

spades3155

/share/singularity/images/ccs/conda/amd-conda9-rocky8.sinf

singularity run --app spades3155 /share/singularity/images/ccs/conda/amd-conda9-rocky8.sinf spades.py --test

EarlGrey-1.3

earlGrey

/share/singularity/images/ccs/EarlGrey/earlgrey-docker.sinf

singularity exec /share/singularity/images/ccs/EarlGrey/earlgrey-docker.sinf earlGrey

verkko-1.2

verkko12

/share/singularity/images/ccs/conda/amd-conda9-rocky8.sinf

singularity run --app verkko12 /share/singularity/images/ccs/conda/amd-conda9-rocky8.sinf verkko

clust-1.18.1

clust1181

/share/singularity/images/ccs/conda/amd-conda9-rocky8.sinf

singularity run --app clust1181 /share/singularity/images/ccs/conda/amd-conda9-rocky8.sinf python /usr/local/clust-1.18.1/clust.py

paraview-5.11.0

paraview5110

share/singularity/images/ccs/conda/amd-conda9-rocky8.sinf

singularity run --app paraview5110 /share/singularity/images/ccs/conda/amd-conda9-rocky8.sinf python

lftp-4.9.2

lftp492

/share/singularity/images/ccs/conda/amd-conda9-rocky8.sinf

singularity run --app lftp492 /share/singularity/images/ccs/conda/amd-conda9-rocky8.sinf lftp -h

isoseq3-3.8.2

isoseq3382

/share/singularity/images/ccs/conda/amd-conda9-rocky8.sinf

singularity run --app isoseq3382 /share/singularity/images/ccs/conda/amd-conda9-rocky8.sinf isoseq3

sibeliaz-1.2.5

ibeliaz125

/share/singularity/images/ccs/conda/amd-conda9-rocky8.sinf

singularity run --app sibeliaz125 /share/singularity/images/ccs/conda/amd-conda9-rocky8.sinf sibeliaz

ensembl-vep-109.3


/share/singularity/images/ccs/dockerhub/ensemble-vep-109.3.sinf

singularity exec /share/singularity/images/ccs/dockerhub/ensemble-vep-109.3.sinf vep

busco-5.4.6

busco546

/share/singularity/images/ccs/conda/amd-conda10-rocky8.sinf

singularity run --app busco546 /share/singularity/images/ccs/conda/amd-conda10-rocky8.sinf busco

finestructure-2.1.3

finestructure213

/share/singularity/images/ccs/conda/amd-conda10-rocky8.sinf

singularity run --app finestructure213 /share/singularity/images/ccs/conda/amd-conda10-rocky8.sinf fs -h

anvio-7.1

anvio71

/share/singularity/images/ccs/conda/amd-conda10-rocky8.sinf

singularity run --app anvio71 /share/singularity/images/ccs/conda/amd-conda10-rocky8.sinf anvi-setup-ncbi-cogs

uLTRA-0.0.4.2

ultra

/share/singularity/images/ccs/conda/amd-conda11-rocky8.sinf

singularity run --app ultra /share/singularity/images/ccs/conda/amd-conda11-rocky8.sinf uLTRA

ccs-6.4.0

ccs640

/share/singularity/images/ccs/conda/amd-conda11-rocky8.sinf

singularity run --app pbccs640 /share/singularity/images/ccs/conda/amd-conda11-rocky8.sinf ccs

lima-2.7.1

lima271

/share/singularity/images/ccs/conda/amd-conda11-rocky8.sinf

singularity run --app lima271 /share/singularity/images/ccs/conda/amd-conda11-rocky8.sinf lima

plascad-1.17

plascad117

/share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinf

singularity run --app plascad117 /share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinf Plascad

braker3


/share/singularity/images/ccs/braker/braker3.sinf

singularity exec /share/singularity/images/ccs/braker/braker3.sinf braker.pl [ See https://hub.docker.com/r/teambraker/braker3]

BisSNP-1.0.1

bissnp101

/share/singularity/images/ccs/conda/amd-conda11-rocky8.sinf

singularity run --app bissnp101 /share/singularity/images/ccs/conda/amd-conda11-rocky8.sinf bis-snp

spaceranger-2.0.1

spaceranger201

/share/singularity/images/ccs/conda/amd-conda12-rocky8.sinf

singularity run --app spaceranger201 /share/singularity/images/ccs/conda/amd-conda12-rocky8.sinf spaceranger

mothur-1.48.0

mothur1480

/share/singularity/images/ccs/conda/amd-conda12-rocky8.sinf

singularity run --app mothur1480 /share/singularity/images/ccs/conda/amd-conda12-rocky8.sinf mothur

trim-galore-0.6.10

trimgalore0610

/share/singularity/images/ccs/conda/amd-conda12-rocky8.sinf

singularity run --app trimgalore0610 /share/singularity/images/ccs/conda/amd-conda12-rocky8.sinf trim_galore

pandas, biopython and pyvcf

pyvcf068dev0

/share/singularity/images/ccs/conda//amd-conda12-rocky8.sinf

singularity run --app pyvcf068dev0 /share/singularity/images/ccs/conda//amd-conda12-rocky8.sinf

bwa-mem2-2.2.1

bwamem2221

/share/singularity/images/ccs/conda/amd-conda12-rocky8.sinf

singularity run --app bwamem2221 /share/singularity/images/ccs/conda/amd-conda12-rocky8.sinf bwa-mem2

metabat2-2.15

metabat2215

/share/singularity/images/ccs/conda//amd-conda12-rocky8.sinf

singularity run --app metabat2215 /share/singularity/images/ccs/conda//amd-conda12-rocky8.sinf metabat2

verkko-1.4

verkko14

/share/singularity/images/ccs/conda/amd-conda12-rocky8.sinf

singularity run --app verkko14 /share/singularity/images/ccs/conda/amd-conda12-rocky8.sinf verkko

nanoplot-1.41.6

nanoplot1416

/share/singularity/images/ccs/conda/amd-conda11-rocky8.sinf

singularity run --app nanoplot1416 /share/singularity/images/ccs/conda/amd-conda11-rocky8.sinf NanoPlot

dorado-0.3.2+d8660a3

dorado032

/share/singularity/images/ccs/conda/amd-conda11-rocky8.sinf

singularity run --app dorado032 /share/singularity/images/ccs/conda/amd-conda11-rocky8.sinf dorado

methpipe-5.0.1

methpipe501

share/singularity/images/ccs/conda/amd-conda13-rocky8.sinf

singularity run --app methpipe501 /share/singularity/images/ccs/conda/amd-conda13-rocky8.sinf methcounts

hifiasm-0.19.6

hifiasm0196

/share/singularity/images/ccs/conda/amd-conda13-rocky8.sinf

singularity run --app hifiasm0196 /share/singularity/images/ccs/conda/amd-conda13-rocky8.sinf hifiasm

phasebook

phasebook

/share/singularity/images/ccs/conda/amd-conda13-rocky8.sinf

singularity run --app phasebook /share/singularity/images/ccs/conda/amd-conda13-rocky8.sinf python /usr/local/phasebook/scripts/phasebook.py -h

idr-2.0.2

idr202

/share/singularity/images/ccs/conda/amd-conda13-rocky8.sinf

singularity run --app idr202 /share/singularity/images/ccs/conda/amd-conda13-rocky8.sinf idr

openmm-8.0.0

openmm800

/share/singularity/images/ccs/conda/amd-conda13-rocky8.sinf

singularity run --app openmm800 /share/singularity/images/ccs/conda/amd-conda13-rocky8.sinf python -m openmm.testInstallation

Eagle_v2.4.1

eaglev241

/share/singularity/images/ccs/conda/amd-conda13-rocky8.sinf

singularity run --app eaglev241 /share/singularity/images/ccs/conda/amd-conda13-rocky8.sinf eagle

spaceranger-2.1.0

spaceranger210

/share/singularity/images/ccs/conda/amd-conda13-rocky8.sinf

singularity run --app spaceranger210 /share/singularity/images/ccs/conda/amd-conda13-rocky8.sinf spaceranger

Meshlab-2020.09


/share/singularity/images/ccs/meshlab/meshlab.sinf

singularity exec /share/singularity/images/ccs/meshlab/meshlab.sinf meshlab

pymeshlab-2022.2.post4


/share/singularity/images/ccs/meshlab/meshlab.sinf

singularity exec /share/singularity/images/ccs/meshlab/meshlab.sinf python3

bcftool-1.18

bcftools118

share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf

singularity run --app bcftools118 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf bcftools

fastx_toolkit-0.0.14

fastxtoolkit0014 

share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf

singularity run --app fastxtoolkit0014 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf fastx_trimmer 

stacks-2.65

stacks265

share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf

singularity run --app stacks265 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf sstacks

stitch-1.6.10

stitch

/share/singularity/images/ccs/stitch/stitch.sinf

wget https://www.well.ox.ac.uk/~rwdavies/ancillary/STITCH_example_2016_05_10.tgz

singularity run --app stitch /share/singularity/images/ccs/stitch/stitch.sinf /usr/local/STITCH/STITCH.R --chr=chr19 --bamlist=bamlist.txt --posfile=pos.txt --genfile=gen.txt --outputdir=./ --K=4 --nGen=100 --nCores=1

masurca-4.1.0

masurca410

/share/singularity/ccs/conda/amd-conda3-rocky8.sinf

singularity run --app masurca410 /share/singularity/images/ccs/conda/amd-conda3-rocky8.sinf masurca

raxml-ng-1.2.0

raxmlng120 

/share/singularity/ccs/conda/amd-conda3-rocky8.sinf

singularity run --app raxmlng120 /share/singularity/images/ccs/conda/amd-conda3-rocky8.sinf raxml-ng

pbbm2-1.13.1

pbmm21131

/share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf

singularity run --app pbmm21131 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf pbmm2

moose-2023-11-08

moose

/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'

openmm-8.1.0 + OpenMiChroM

openmm810

/share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf

singularity run --app openmm810 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf python -m openmm.testInstallation

tetools-1.88

tetools188

/share/singularity/images/ccs/tetools/tetools-1.88.sinf

singularity run --app tetools188 /share/singularity/images/ccs/tetools/tetools-1.88.sinf RepeatMasker

pggb-0.5.4

pggb054

share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf

singularity run --app pggb054 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf pggb

lefse-1.1.2

lefse

/share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf

singularity run -app lefse112 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf lefse

gfacpp

gfacpp

/share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf

singularity run --app gfacpp /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf bubble_removal

qiime2-2023.9

qiime220239

/share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf

singularity run --app qiime220239 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf qiime

prism-0.9

prism-gain, prism-clust, prism-decom

/share/singularity/images/ccs/prism/ccs-prism-rocky8.sif

singularity run -e /share/singularity/images/ccs/prism/ccs-prism-rocky8.sif --env OMP_NUM_THREADS=$NUM_THREADS bash -c './test_simple.sh'

checkm-genome-1.2.2

checkmgenome122

/share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf

singularity run --app checkmgenome122 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf checkm

homer-4.11

homer411

/share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf

singularity run --app homer411 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf homer

gtdbtk-2.3.2

gtdbtk232

/share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf

singularity run --app gtdbtk232 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf gtdbtk

gangstr-2.5.0

gangstr250

/share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf

singularity run --app gangstr250 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf GangSTR --help

vcflib-1.0.9

vcflib109

/share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf

singularity run --app vcflib109 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf

vcflib-1.0.3

vcflib103

/share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf

singularity run --app vcflib103 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf

qiime2-2024.2

qiime220242

/share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf

singularity run --app qiime220242 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf qiime

r-seurat-5.0.1

rseurat501

/share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf

singularity run --app rseurat501 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf R

busco-5.7.0busco570/share/singularity/images/ccs/conda/amd-conda14-rocky8.sinfsingularity run --app busco570 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf busco
longstitch-1.0.5 longstitch105/share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf singularity run --app longstitch105 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf longstitch
Spaceranger-3.0.0spaceranger300/share/singularity/images/ccs/conda/amd-conda14-rocky8.sinfsingularity run --app spaceranger300 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf spaceranger
vcf2ArlequinDiploidvcf2ArlequinDiploid /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf singularity run --app VCF2ArlequinDiploid /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf python /usr/local/VCF2ArlequinDiploid/vcf2ArlequinDiploid.py
fastStructurefastStructure10 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf singularity run --app fastStructure10 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf structure.py
TRToolstrtools601/share/singularity/images/ccs/conda/amd-conda14-rocky8.sinfsingularity run --app trtools601 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf mergeSTR
GLnexusglnexus1413/share/singularity/images/ccs/conda/amd-conda14-rocky8.sinfsingularity run --app glnexus1413 /share/singularity/images/ccs/conda/amd-conda14-rocky8.sinf glnexus_cli
PICRUSt2picrust2252/share/singularity/images/ccs/conda/amd-conda15-rocky8.sinfsingularity run --app picrust2252 /share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf picrust2_pipeline.py

ADMIXTURE-1.3.0

admixture130/share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf

singularity run --app admixture130 /share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf admixture --help

GTDB-Tk-2.4.0gtdbtk240/share/singularity/images/ccs/conda/amd-conda15-rocky8.sinfsingularity run --env GTDBTK_DATA_PATH=/gtdbtk_data/database -B /share/examples/MCC/gtdbtk/release220:/gtdbtk_data/database --app gtdbtk240 /share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf gtdbtk check_install
HUMAnN-3.9humann39/share/singularity/images/ccs/conda/amd-conda15-rocky8.sinfsingularity run --app humann39 /share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf humann --version
MetaPhlAn-4.1.0metaphlan410/share/singularity/images/ccs/conda/amd-conda15-rocky8.sinfsingularity run --app metaphlan410 --env METAPHLAN_DB_DIR=/share/apps/amd/MetaPhlAn/databases/ /share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf metaphlan --version
SoloTTE-1.09solote109/share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf

singularity run --app solote109 /share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf python /usr/local/Miniconda3/envs/solote-1.09/bin/SoloTE_pipeline.py -h

RDKit-2024.03.1, pandas-2.2.2


rdkit2024031/share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf

singularity run --app rdkit2024031 /share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf python

import pandas as pd; print ("Pandas version:", pd.__version__); from rdkit import Chem; print ("RDKit version:", Chem.rdBase.rdkitVersion)

galba-1.0.11
/share/singularity/images/ccs/galba/galba.sinf

singularity exec /share/singularity/images/ccs/galba/galba.sinf galba.pl --help

fastp-0.23.4fastp0234/share/singularity/images/ccs/conda/amd-conda15-rocky8.sinfsingularity run --app fastp0234 /share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf fastp --version

hifiasm-v0.19.9

hifiasm0199

/share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf

singularity run --app hifiasm0199 /share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf hifiasm -v

compleasm-v0.2.6

compleasm026

/share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf

singularity run --app compleasm026 /share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf compleasm -v

hmmer-v3.4hmmer34/share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf

singularity run --app hmmer34 /share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf hmmbuild -h

mosdepth-v0.3.8mosdepth038/share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf

singularity run --app mosdepth038 /share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf mosdepth --version

verkko-v2.0verkko20/share/singularity/images/ccs/conda/amd-conda15-rocky8.sinfsingularity run --app verkko20 /share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf verkko --help
cellranger-v8.0.0

cellranger800

/share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf

singularity run --app cellranger800 /share/singularity/images/ccs/conda/amd-conda15-rocky8.sinf cellranger -h

EnTAP v1.1.0
/share/singularity/images/ccs/entap/entap.sinf

singularity run /share/singularity/images/ccs/entap/entap.sinf EnTAP -h

scTE v1.0.0scte100/share/singularity/images/ccs/conda/amd-conda16-rocky8.sinf

singularity run --app scte100 /share/singularity/images/ccs/conda/amd-conda16-rocky8.sinf scTE -h

FCS-GX v0.4.0python3 fcs-gx.py/share/singularity/images/ccs/FCS-GX/gcs-gx.sifSee examples in /share/examples/MCC/fcs/gx/ for how to run. Likewise, see examples in /share/examples/MCC/fcs/adaptor/ for the FCS-Adaptor script.
singlem-0.18.0singlem0180/share/singularity/images/ccs/conda/amd-conda16-rocky8.sinf singularity run --app singlem0180 /share/singularity/images/ccs/conda/amd-conda16-rocky8.sinf singlem
blobtools v1.1.1blobtools111/share/singularity/images/ccs/conda/amd-conda16-rocky8.sinf

singularity run --app blobtools111 -B {path_to_git_cloned_blobtools}:/usr/local/blobtools-blobtools_v1.1.1 /share/singularity/images/ccs/conda/amd-conda16-rocky8.sinf bash -c "cd /usr/local//blobtools-blobtools_v1.1.1 && blobtools --help"

glimpse v2.0.0glimpse200/share/singularity/images/ccs/conda/amd-conda16-rocky8.sinfsingularity run --app glimpse200 /share/singularity/images/ccs/conda/amd-conda16-rocky8.sinf GLIMPSE2_chunk --help
glimpse v2.0.1glimpse201/share/singularity/images/ccs/conda/amd-conda16-rocky8.sinfsingularity run --app glimpse201 /share/singularity/images/ccs/conda/amd-conda16-rocky8.sinf GLIMPSE2_chunk --help
plink2 v2.00a5.12

plink2200a512

/share/singularity/images/ccs/conda/amd-conda16-rocky8.sinf

singularity run --app plink2200a512 /share/singularity/images/ccs/conda/amd-conda16-rocky8.sinf plink2 --version

rvtests v2.1.0rvtests210/share/singularity/images/ccs/rvtests/amd-rvtests-rocky9.sinfsingularity run --app rvtests210 /share/singularity/images/ccs/rvtests/amd-rvtests-rocky9.sinf rvtest --help
BayeScan v2.1bayescan21/share/singularity/images/ccs/conda/amd-conda16-rocky8.sinfsingularity run --app bayescan21 /share/singularity/images/ccs/conda/amd-conda16-rocky8.sinf bayescan_2.1 --help
assembly-stats-1.01assemblystats101/share/singularity/images/ccs/conda/amd-conda16-rocky8.sinfsingularity run --app assemblystats101 /share/singularity/images/ccs/conda/amd-conda16-rocky8.sinf assembly-stats
structure-threader v1.3.11structure_threader1311/share/singularity/images/ccs/conda/amd-conda16-rocky8.sinf
singularity run --app structure_threader1311 /share/singularity/images/ccs/conda/amd-conda16-rocky8.sinf structure_threader --help
starfish v1.0.0starfish100/share/singularity/images/ccs/conda/amd-conda16-rocky8.sinfsingularity run --app starfish100 /share/singularity/images/ccs/conda/amd-conda16-rocky8.sinf starfish --help
rnabloom v2.0.1rnabloom201/share/singularity/images/ccs/conda/amd-conda16-rocky8.sinfsingularity run --app rnabloom201 /share/singularity/images/ccs/conda/amd-conda16-rocky8.sinf rnabloom --help
DsuiteDsuite/share/singularity/images/ccs/conda/amd-conda16-rocky8.sinfsingularity run --app Dsuite /share/singularity/images/ccs/conda/amd-conda16-rocky8.sinf Dsuite Dtrios --help
isoseq v4.0.0, lima v2.9.0, pbskera v1.2.0isoseq400/share/singularity/images/ccs/conda/amd-conda17-rocky8.sinf

singularity run --app isoseq400 /share/singularity/images/ccs/conda/amd-conda17-rocky8.sinf isoseq --help

BBMap_39.08bbmap3908/share/singularity/images/ccs/conda/amd-conda17-rocky8.sinf singularity run --app bbmap3908 /share/singularity/images/ccs/conda/amd-conda17-rocky8.sinf bbduk.sh
Verkko v2.2verkko22/share/singularity/images/ccs/conda/amd-conda17-rocky8.sinf singularity run --app verkko22 /share/singularity/images/ccs/conda/amd-conda17-rocky8.sinf verkko --help
Funannotate v1.8.17funannotate1817/share/singularity/images/ccs/conda/amd-conda17-rocky8.sinf singularity run --app funannotate1817 /share/singularity/images/ccs/conda/amd-conda17-rocky8.sinf funannotate --help
cellbender-0.3.0cellbender030/share/singularity/images/ccs/conda/amd-conda17-rocky8.sinf singularity run --app cellbender030 /share/singularity/images/ccs/conda/amd-conda17-rocky8.sinf cellbender
kaiju-1.10.1kaiju1101/share/singularity/images/ccs/conda/amd-conda17-rocky8.sinfsingularity run --app kaiju1101 /share/singularity/images/ccs/conda/amd-conda17-rocky8.sinf kaiju
gapless-0.4-0gapless040/share/singularity/images/ccs/conda/amd-conda18-rocky8.sinfsingularity run --app gapless040 /share/singularity/images/ccs/conda/amd-conda18-rocky8.sinf gapless.sh -h
ntLink-1.3.10-2ntlink13102/share/singularity/images/ccs/conda/amd-conda18-rocky8.sinfsingularity run --app ntlink13102 /share/singularity/images/ccs/conda/amd-conda18-rocky8.sinf ntLink help
RevBaye-1.2.4
/share/singularity/images/ccs/revbayes/revbayes-v1.2.4-linux64-singularity.sinf

singularity exec /share/singularity/images/ccs/revbayes/revbayes-v1.2.4-linux64-singularity.sinf rb yourscript (serial)


singularity exec /share/singularity/images/ccs/revbayes/revbayes-v1.2.4-linux64-singularity.sinf mpiexec -n XX rb-mpi yourscript (parallel, XX=# of cores)

bioperl-1.7.8perlbioperl178/share/singularity/images/ccs/conda/amd-conda18-rocky8.sinfsingularity run --app perlbioperl178 /share/singularity/images/ccs/conda/amd-conda18-rocky8.sinf perl -MBio::SeqIO -e 'print "Bio::SeqIO is installed\n"'
parallel-20240922gnuparallel20240922/share/singularity/images/ccs/conda/amd-conda18-rocky8.sinfsingularity run --app gnuparallel20240922 /share/singularity/images/ccs/conda/amd-conda18-rocky8.sinf parallel --help
canu-2.2-0canu220/share/singularity/images/ccs/conda/amd-conda18-rocky8.sinfsingularity run --app canu220 /share/singularity/images/ccs/conda/amd-conda18-rocky8.sinf canu --help
bioawk-1.0bioawk10/share/singularity/images/ccs/conda/amd-conda18-rocky8.sinfsingularity run --app bioawk10 /share/singularity/images/ccs/conda/amd-conda18-rocky8.sinf bioawk
exceRpt v5.0
/share/singularity/images/ccs/exceRpt/amd-exceRpt.sinf

singularity run -B /share/examples/MCC/exceRpt/input:/exceRptInput -B /share/examples/MCC/exceRpt/output:/exceRptOutput -B /share/examples/MCC/exceRpt/database/hg38:/exceRpt_DB/hg38 /share/singularity/images/ccs/exceRpt/amd-exceRpt.sinf INPUT_FILE_PATH=/exceRptInput/SRR026761.sra N_THREADS=16

See example at /share/examples/MCC/exceRpt/

raxml-ng v1.2.2 (MPI)
/share/singularity/images/ccs/raxml-ng-mpi/amd-raxml-ng-mpi.sinf

mpirun -n 4 singularity exec /share/singularity/images/ccs/raxml-ng-mpi/amd-raxml-ng-mpi.sinf raxml-ng-mpi --msa rbcl.phy --model GTR+G --prefix H1 --threads 16 --extra thread-nopin --force perf_threads

See example at /share/examples/MCC/raxml-ng-mpi

BIONANO Solve v3.5.1 (with runBNG)
/share/singularity/images/ccs/runBNG-BIONANO/amd-runBNG-centos7.sinf

singularity run /share/singularity/images/ccs/runBNG-BIONANO/amd-runBNG-centos7.sinf runBNG

See example at /share/examples/MCC/runBNG-BIONANO

fmriprep v24.4.1
/share/singularity/images/ccs/fmriprep/amd-fmriprep-24.4.1.sinfsingularity run /share/singularity/images/ccs/fmriprep/amd-fmriprep-24.4.1.sinf path/to/data/dir path/to/output/dir participant --participant-label label
megahit v1.2.9-5megahit1295/share/singularity/images/ccs/conda/amd-conda18-rocky8.sinfsingularity run --app megahit1295 /share/singularity/images/ccs/conda/amd-conda18-rocky8.sinf megahit --help
prodigal v2.6.3-9prodigal2639/share/singularity/images/ccs/conda/amd-conda18-rocky8.sinfsingularity run --app prodigal2639 /share/singularity/images/ccs/conda/amd-conda18-rocky8.sinf prodigal --help
pyani v0.2.13.1-0pyani021310/share/singularity/images/ccs/conda/amd-conda18-rocky8.sinfsingularity run --app pyani021310 /share/singularity/images/ccs/conda/amd-conda18-rocky8.sinf pyani --help
kraken2 v2.1.3-2kraken22132/share/singularity/images/ccs/conda/amd-conda18-rocky8.sinfsingularity run --app kraken22132 /share/singularity/images/ccs/conda/amd-conda18-rocky8.sinf kraken2 --help
spaceranger v3.1.2spaceranger312/share/singularity/images/ccs/conda/amd-conda18-rocky8.sinfsingularity run --app spaceranger312 /share/singularity/images/ccs/conda/amd-conda18-rocky8.sinf spaceranger --help
braker3 v3.0.7.6
/share/singularity/images/ccs/braker/braker3-3.0.7.6.sinfsingularity exec /share/singularity/images/ccs/braker/braker3-3.0.7.6.sinf braker.pl [ See https://hub.docker.com/r/teambraker/braker3]
RAiSDraisd/share/singularity/images/ccs/conda/amd-conda19-rocky9.sinfsingularity run --app raisd /share/singularity/images/ccs/conda/amd-conda19-rocky9.sinf RAiSD -h
vibrant v1.2.1-4vibrant1214/share/singularity/images/ccs/conda/amd-conda19-rocky9.sinfsingularity run --app vibrant1214 /share/singularity/images/ccs/conda/amd-conda19-rocky9.sinf vibrant --help
check v1.0.3-0checkv1030/share/singularity/images/ccs/conda/amd-conda19-rocky9.sinfsingularity run --app checkv1030 /share/singularity/images/ccs/conda/amd-conda19-rocky9.sinf checkv --help
coverm v0.7.0-1coverm0701/share/singularity/images/ccs/conda/amd-conda19-rocky9.sinfsingularity run --app coverm0701 /share/singularity/images/ccs/conda/amd-conda19-rocky9.sinf coverm --help
vcontact2 v0.11.3-0vcontact20113/share/singularity/images/ccs/conda/amd-conda19-rocky9.sinfsingularity run --app vcontact20113 /share/singularity/images/ccs/conda/amd-conda19-rocky9.sinf vcontact2
iphop v1.3.3-0iphop1330/share/singularity/images/ccs/conda/amd-conda19-rocky9.sinfsingularity run --app iphop1330 /share/singularity/images/ccs/conda/amd-conda19-rocky9.sinf iphop --help
dRep v3.5.0-0drep3500/share/singularity/images/ccs/conda/amd-conda19-rocky9.sinfsingularity run --app drep3500 /share/singularity/images/ccs/conda/amd-conda19-rocky9.sinf dRep --help
vamb v3.0.2-2vamb302/share/singularity/images/ccs/conda/amd-conda19-rocky9.sinf

singularity run --app vamb302 /share/singularity/images/ccs/conda/amd-conda19-rocky9.sinf vamb --help

squigualiser v0.6.3-0squigualiser0630/share/singularity/images/ccs/conda/amd-conda19-rocky9.sinfsingularity run --app squigualiser0630 /share/singularity/images/ccs/conda/amd-conda19-rocky9.sinf squigualiser --help
uncalled4 v4.1.0uncalled4410/share/singularity/images/ccs/conda/amd-conda19-rocky9.sinfsingularity run --app uncalled4410 /share/singularity/images/ccs/conda/amd-conda19-rocky9.sinf uncalled4 --help
slow5tools v1.3.0slow5tools130/share/singularity/images/ccs/conda/amd-conda19-rocky9.sinf

singularity run --app slow5tools130 /share/singularity/images/ccs/conda/amd-conda19-rocky9.sinf slow5tools --help

singularity run --app slow5tools130 /share/singularity/images/ccs/conda/amd-conda19-rocky9.sinf realf2s.sh --help

nanofilt v2.8.0-0nanofilt2800/share/singularity/images/ccs/conda/amd-conda19-rocky9.sinfsingularity run --app nanofilt2800 /share/singularity/images/ccs/conda/amd-conda19-rocky9.sinf NanoFilt --help
chopper v0.9.0-1chopper0901/share/singularity/images/ccs/conda/amd-conda19-rocky9.sinfsingularity run --app chopper0901 /share/singularity/images/ccs/conda/amd-conda19-rocky9.sinf chopper --help
CellRanger v9.0.0cellranger900/share/singularity/images/ccs/conda/amd-conda19-rocky9.sinfsingularity run --app cellranger900 /share/singularity/images/ccs/conda/amd-conda19-rocky9.sinf cellranger --help
liftoff v1.6.3-1liftoff1631/share/singularity/images/ccs/conda/amd-conda19-rocky9.sinfsingularity run --app liftoff1631 /share/singularity/images/ccs/conda/amd-conda19-rocky9.sinf liftoff --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. To use interactively Invoke the singularity container shell.

[user@login001]$ singularity shell  /share/singularity/images/ccs/conda/amd-conda1-centos8.sinf

2. Activate the conda environment for whichever package you want to use, eg blast-2.12.0 

Singularity lcc-conda-1-centos8.sinf :~> Singularity> conda info --envs
# conda environments:
#
/mnt/gpfs3_amd/share/apps/amd/Miniconda3
/share/apps/amd/conda/envs/python-3.9.6
base * /usr/local/Miniconda3
ambertools-21.7 /usr/local/Miniconda3/envs/ambertools-21.7
blast-2.12.0 /usr/local/Miniconda3/envs/blast-2.12.0
minimap-2.22 /usr/local/Miniconda3/envs/minimap-2.22
mirdeep2-2.0.1.2 /usr/local/Miniconda3/envs/mirdeep2-2.0.1.2
plink-1.90b6.21 /usr/local/Miniconda3/envs/plink-1.90b6.21
purge_dups-1.2.5 /usr/local/Miniconda3/envs/purge_dups-1.2.5
pymatgen-2022.0.12 /usr/local/Miniconda3/envs/pymatgen-2022.0.12
pytraj-2.0.5 /usr/local/Miniconda3/envs/pytraj-2.0.5
r-seurat-4.0.4 /usr/local/Miniconda3/envs/r-seurat-4.0.4
sra-tools-2.11.0 /usr/local/Miniconda3/envs/sra-tools-2.11.0
tk-8.6.10 /usr/local/Miniconda3/envs/tk-8.6.10

3. Then use the package as intended(eg: blast-2.12.0)

(samtools-1.10) Singularity lcc-conda-1-centos8.sinf :~> source activate /usr/local/Miniconda3/envs/blast-2.12.0
(blast-2.12.0) Singularity> blastn

4. After usage of that conda package

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

5. 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. cellranger-6.1.1  (The app name to be used for 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=normal                                                                 #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=coa_XXXXX_uksr                                                    #Name of slurm account to run under

#Module needed to run the conda job


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

container=/share/singularity/images/ccs/conda/amd-conda1-centos8.sinf

#blast program execution command (app name is from second column from table above)

singularity run --app blast2120 $container blastn

An example is available in the folder  /share/examples/MCC/conda


               

Center for Computational Sciences