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

Owned by UKY CCS RCD
Nov 16, 2024
7 min read

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


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