Software list for singularity containers for conda packages in the MCC cluster
- UKY CCS RCD
- Vikram Gazula
- Pinyi Shi
- Farmer, Barry
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/ngstsamtools-1.21.sinf ools/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 |
Center for Computational Sciences