Conda and Containers on LCC
- UKY CCS RCD
Owned by UKY CCS RCD
Sept 18, 2024
5 min read
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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 name in the container to be used in the slurm script | Container Name and location | Notes |
|---|---|---|---|
| checkm-genome-1.1.2 | checkm112 | /share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf | |
| deeptools-3.4.3 | deeptools343 | /share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf | |
| ncl-6.6.2 | ncl662 | /share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf | |
| ncview-2.1.7 | ncview217 | /share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf | |
| quast-5.0.2 | quast502 | /share/singularity/images/ccs/conda/lcc-conda-ubuntu-20.04.sinf | |
| roary-3.13.0 | roary3130 | /share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf | |
| samtools-1.10 | samtools110 | /share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf | |
| mummer4-4.0.0beta2 | mummer4400beta2 | /share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf | |
| trinity-2.9.1 | trinity291 | /share/singularity/images/ccs/condls a/lcc-conda-1-centos8.sinf | |
| wrf-python-1.3.2 | wrfpython132 | /share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf | |
| blast-2.10.1 | blast2101 | /share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf | |
| minimap2-2.17 | minimap2217 | /share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf | |
| qiime2-2020.8.0 | qiime2202080 | /share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf | |
| canu-2.1 | canu21 | /share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf | |
| pilon-1.23 | pilon123 | /share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf | |
| lastz-1.0.4 | lastz104 | /share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf | |
| bayescan-2.0.1 | bayescan201 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| hyphy-2.5.17 | hyphy2517 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| macs-2.2.7.1 | macs2271 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| quorum-1.1.1 | quorum111 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| soapdenovo-2.40 | soapdenovo240 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| trinity2110 | trinity-2.11.0 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| fast5-0.6.5 | fast5065 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| fastx_toolkit-0.0.14 | fastx_toolkit0014 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| hisat2.2.1 | hisat221 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| htseq-0.12.4 | htseq0124 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| jellyfish-2.2.10 | jellyfish2210 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| jellyfish-2.2.6 | jellyfish226 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| mirdeep-2.0.1.2 | mirdeep2012 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| mrbayes-3.2.7 | mrbayes327 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| muscle-3.8.1551 | muscle381551 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| paml-4.9 | paml49 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| pcre-8.44 | pcre844 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| plink-1.90b6.12 | plink190b612 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| rnastructure-6.1 | rnastructure61 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| scons-3.1.2 | scons312 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| sra-tools-2.10.8 | sratools2108 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| stacks-2.53 | stacks253 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| star-2.7.5c | star275c | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| tophat-2.1.1 | tophat211 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| vcftools-0.1.16 | vcftools0116 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| velvet-1.2.10 | velvet1210 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | singularity run --app velvet1210 /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf velvetg |
| viennarna-2.4.15 | viennarna2415 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| fastqc-0.11.9 | fastqc0119 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| blast-2.10.1 | blast2101 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| bowtie-2.4.1 | bowtie241 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| bwa-0.7.17 | bwa0717 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| bedtools-2.29.2 | bedtools2292 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| cdhit-4.6.1 | cdhit461 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| mcl-14.137 | mcl14137 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| mafft-7.471 | mafft7471 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| guidance-2.0 | guidance202 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| raxml-8.2.12 | raxml8212 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| bismark-0.22.3 | bismark0223 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| gatk-4.1.8.1 | gatk4181 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf | |
| exonerate-gff3 | exonerategff3 | /share/singularity/images/ccs/conda/lcc-bio-1-centos8.sinf | |
| implicit-landuse | implicitlanduse | /share/singularity/images/ccs/conda/lcc-conda-4-centos8.sinf | |
| gdal-3.1.2 | gdal312 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf | |
| bayescan-2.0.1 | bayescan201 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf | |
| bcftools-1.10.2 | bcftools1102 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf | |
| notebook-6.1.4 (includes pandas,numpy,scikit-learn) | notebook614 | /share/singularity/images/ccs/conda/lcc-conda-4-centos8.sinf | |
| mdanalysis-1.0.0 | mdanalysis | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf | |
| ensembl-vep-101.0 | ensemblvep1010 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf | |
| mothur-1.44.3 | mothur1443 | /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf | |
| mothur-1.44.11 | mothur14411 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf | |
| openbabel-2.4.1 | openbabel241 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf | |
| structure-2.3.4 | structure234 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf | |
| mega-10.1.8-1 | megax10181 | /share/singularity/images/ccs/MEGA/lcc-mega-10.1.8-1-centos8.sinf | |
| bcftools-1.11 (includes samtools-1.11) | bcftools111 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf | |
| minigraph | minigraph | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf | |
| annoy-1.17.0 | annoy1170 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf | |
| lammpss-deepmd-kit-module-gpu | lammpssdkmg | /share/singularity/images/ccs/conda/lcc-conda-4-centos8.sinf | |
| lammpss-deepmd-kit-module-cpu | lammpssdkmc | /share/singularity/images/ccs/conda/lcc-conda-4-centos8.sinf | |
| busco-5.0.0 | busco500 | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf | singularity run --app busco500 /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf busco |
| SigProfilerExtractor | SigProfilerExtractor | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf | |
| transdecoder-5.5.0 | transdecoder550 | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf | |
| transrate-tools-1.0.0 | transratetools100 | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf | |
| transrate-1.0.3 | transrate103 | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf | |
| detonate-1.11 | detonate111 | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf | |
| SPlisHSPlasH | SPlisHSPlasH | /share/singularity/images/ccs/splishsplash/SPlisHSPlasH.sinf | |
| cd-hit-4.8.1 | cdhit481 | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf | |
| cd-hit-auxtools-4.8.1 | cdhitauxtools481 | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf | |
| dask-2021.2.0 | dask202120 | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf | |
| dask-distributed-2021.2.0 | daskdistributed202120 | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf | |
| canu-2.1.1 | canu211 | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf | |
| pb-assembly | pbassembly | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf | |
| braker | braker | /share/singularity/images/ccs/braker/braker.sinf | |
| blasr-5.3.5 | blasr535 | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf | |
| megahit-1.2.9 | megahit129 | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf | |
| trimmomatic-0.39 | trimmomatic039 | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf | |
| mitoz | mitoz | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf | |
| methyldackel-0.5.2 | methyldackel052 | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf | |
qiime2-2021.2 | qiime220212 | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf | |
| pbjelly | pbjelly | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf | |
| rnammer-1.2 | rnammer12 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf | |
| tmhmm-2.0c | tmhmm20c | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf | |
| signalp-4.1 | signalP41 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf | |
| bioconductor-dss-2.38.0 | bioconductordss2380 | /share/singularity/images/ccs/conda/lcc-conda-R-1-centos8.sinf | |
| r-peer-1.3 | rpeer13 | /share/singularity/images/ccs/conda/lcc-conda-R-conda-centos8.sinf | |
| pytraj-2.0.4 | pytraj204 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf | |
| busco-5.1.2 | busco512 | /share/singularity/images/ccs/conda/lcc-conda-7-centos8.sinf | |
| bowtie2-2.3.5-sra-linux | bowtie235sralinux | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf | |
| bowtie-2.4.2 | bowtie242 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf | |
| mdtraj-1.9.5 | mdtraj195 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf | |
| mothur-1.45.2 | mothur1452 | /share/singularity/images/ccs/conda/lcc-bio-1-centos8.sinf | |
| breakdancer-1.4.5 | breakdancer145 | /share/singularity/images/ccs/conda/lcc-docker-break-dancer.sinf | |
| lima-2.0.0 | lima200 | /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf | |
| bedops-2.4.39 | bedops2439 | /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf | |
| ambertools-20.15 | amber2015 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf | |
| tama | tama | /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf | |
| cdna_cupcake-22.0.0 | cdnacupcake2200 | /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf | |
| reindeer | REINDEER | /share/singularity/images/ccs/conda/lcc-conda-4-centos8.sinf | |
| SQANTI3 | SQANTI3 | /share/singularity/images/ccs/conda/lcc-conda-4-centos8.sinf | |
| mothur-1.45.3 | mothur1453 | /share/singularity/images/ccs/conda/lcc-bio-1-centos8.sinf | |
| bismark-0.23.0 | bismark0230 | /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf | |
| hmmer-3.3.2 | hmmer332 | /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf | |
| humann-3.0.0.alpha.1 | humann300alpha1 | /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf | |
| velvet-1.2.10 | velvet1210 | /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf | singularity run --app velvet1210 /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf velvetg |
| pretext-suite-0.0.2 | pretextsuite002 | /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf | |
| tetools-1.4 | tetools14 | /share/singularity/images/ccs/tetools/tetools-1.4.sinf | |
| trinityrnaseq-2.12.0 | trinityrnaseq2120 | /share/singularity/images/ccs/conda/trinityrnaseq-2.12.0.sinf | |
| GFF3toolkit-2.0.3 | GFF3toolkit | /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf | |
| getorganelle-1.7.5.0 | getorganelle1750 | /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf | |
| mitobim-1.9.1 | mitobim | /share/singularity/images/ccs/conda/MITObim.sinf | |
| r-wgcna-1.69 | rwgcna169 | /share/singularity/images/ccs/conda/lcc-r-1-centos7-test.sinf | |
| tpmcalculator-0.0.4 | tpmalculator004 | /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf | |
| novoplasty-4.2 | novoplasty42 | /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf | |
| mitofinder-1.4 | mitofinder14 | /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf | |
| velvetoptimiser-2.2.6 | velvetoptimiser226 | /share/singularity/images/ccs/conda/./lcc-bio-1-centos7.sinf | singularity run --app velvetoptimiser226 /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf VelvetOptimiser.pl |
| jags-4.3.0 | jags430 | /share/singularity/images/ccs/conda/./lcc-bio-1-centos7.sinf | |
| qiime2-2021.8 | qiime220218 | /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf | |
| perl-bioperl-1.7.2 | bioperl172 | /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf | |
| ancestry_hmm | ancestry_hmm | /share/singularity/images/ccs/ancestry_HMM/armadillo-ancestry_hmm.sinf | |
| MARTY1-3 | marty13 | /share/singularity/images/ccs/MARTY/1.3/marty-1.3.sinf | |
| ngsTools | ngsTools | /share/singularity/images/ccs/ngsTools/ngsTools.sinf | includes bcftools-1.9, samtools-1.9, htslib-1.9 (from older versions combined) |
| spades-3.15.3 | spades3153 | /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf | |
| ngsutils-0.5.9 | ngsutils059 | /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf | |
| bcftools-1.13 | bcftools113 | /share/singularity/images/ccs/ngsTools/samtools-1.13+matplotlib-bcftoools-1.13.sinf | |
| samtools-1.13 | samtools113 | /share/singularity/images/ccs/ngsTools/samtools-1.13+matplotlib-bcftoools-1.13.sinf | |
| angsd-0.910 | angsd0910 | /share/singularity/images/ccs/conda/lcc-conda-6-cento8.sinf | |
| angsd-0.935 | angsd0935 | /share/singularity/images/ccs/conda/lcc-conda-6-cento8.sinf | |
| ensembl-vep-104.3 | ensemblvep1043 | /share/singularity/images/ccs/conda/lcc-conda-6-cento8.sinf | |
| angsd-0.931 | angsd0931 | /share/singularity/images/ccs/conda/lcc-conda-6-cento8.sinf | |
| freebayes-1.3.4 | freebayes134 | /share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf | |
| mashtree-1.2.0 | mashtree120 | /share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf | |
| prokka1146 | prokka1146 | /share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf | |
| angsd-0.933 | angsd0933 | /share/singularity/images/ccs/conda/lcc-conda-6-cento8.sinf | |
| pybind11-2.8.0 | pybind11280 | /share/singularity/images/ccs/conda/lcc-conda-6-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 |
| mmseqs2-13.45111 | mmseqs21345111 | /share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf | |
| svim-asm-1.0.2 | svimasm102 | /share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf | includes minimap2 and samtools |
| pacbio | pacbio | /share/singularity/images/ccs/pacbio/pacbio.sinf | lima,pbccs,isoseq3 |
| gtf2csv | gtf2csv | /share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf | singularity run --app gtf2csv /share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf gtf2csv |
| phyml-3.3.20200621 | phyml3320200621 | /share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf | |
| cactus-2.0.4 | /share/singularity/images/ccs/cactus/cactus-2.0.4.sinf | see /share/examples/LCC/cactus | |
| pbmm2-1.7.0 | pbmm2170 | /share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf | |
| ragtag-2.1.0 | ragtag210 | /share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf | |
| minimap2-2.24 | minimap2224 | /share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf | |
| gmap-2021.08.25 | gmap20210825 | /share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf | singularity run --app gmap20210825 /share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf gmap |
| sabre-1.000 | sabre1000 | /share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf | singularity run --app sabre1000 /share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf sabre |
| deepchem-2.5.0 | deepchem250 | /share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf | singularity run --app deepchem250 /share/singularity/images/ccs/conda/lcc-conda-6-centos8.sinf python |
| adapterremoval-2.3.2 | adapterremoval232 | /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf | singularity run --app adapterremoval232 /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf AdapterRemoval |
| deepchem-2.6.1-GPU | deepchem261gpu | /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf | module load ccs/singularity module load ccs/cuda/11.2.0_460.27.04 singularity run --app deepchem261gpu --nv /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf python |
| salmon-1.6.0 | salmon160 | /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf | singularity run --app salmon160 /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf salmon |
| 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 |
| metaphlan-3.0.14 | metaphlan3014 | /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf | singularity run --app metaphlan3014 /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf metaphlan |
| biobakery_workflows-3.0.0a7 | biobakeryworkflows300a7 | /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf | singularity run --app biobakeryworkflows300a7 /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf biobakery_workflows_databases |
| humann2-2.8.1 | humann2281 | /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf | singularity run --app humann2281 /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf humann2 |
| phylophlan302 | phylophlan302 | /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf | singularity run --app phylophlan302 /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf phylophlan |
| maaslin2-0.99.12 | maaslin209912 | /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf | *Invoke through R |
| kneaddata-0.10.0 | kneaddata0100 | /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf | singularity run --app kneaddata0100 /share/singularity/images/ccs/conda/lcc-conda-1-rocky8.sinf kneaddata |
| velocyto-0.17 | velocyto017 | /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf | singularity run --app velocyto017 /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf velocyto |
| mpdaf-3.5 and fitsio-1.1.7 | mpdaf35fitsio117 | /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf | singularity run --app mpdaf35fitsio117 /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf python |
| afterqc-0.9.7 | afterqc097 | /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf | singularity run --app afterqc097 /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf python /usr/local/Miniconda3/envs/afterqc-0.9.7/bin/after.py -1 R1.fq.gz |
| hmmer2go | hmmer2go | /share/singularity/images/ccs/hmmer2go/hmmer2go.sinf | singularity run --app hmmer2go /share/singularity/images/ccs/hmmer2go/hmmer2go.sinf hmmer2go |
| cgmaptools | cgmaptools | /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf | singularity run --app cgmaptools /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf cgmaptools |
| cutadapt-3.7 | cutadapt37 | /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf | singularity run --app cutadapt37 /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf cutadapt |
| fastx_toolkit-0.0.14 | fastxtoolkit00147 | /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf | singularity run --app fastxtoolkit00147 /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf fastq_to_fasta |
| Dsuite | Dsuite | /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf | singularity run --app Dsuite /share/singularity/images/ccs/conda/lcc-conda-2-rocky8.sinf Dsuite |
| variantbam-1.4.4a | variantbam144a | /share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinf | singularity run --app variantbam144a /share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinf variant |
| qiskit-0.36.2 | qiskit0362 | /share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinf | singularity run --app qiskit0362 /share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinf python |
| crackling | crackling | /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 -c config.ini (location of default config.ini in the container is /usr/local/Crackling/config.ini |
| gist-pipeline | gistpipeline | /share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinf | singularity run --app gistpipeline /share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinf gistPipeline |
| inotify-tools-3.20.2 | notifytools3202 | share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinf | singularity run --app inotifytools3202 /share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinf inotifywatch |
| parallel-20220722 | parallel20220722 | share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinf | singularity run --app parallel20220722 /share/singularity/images/ccs/conda/lcc-conda-3-rocky8.sinf parallel |
| NRI-MD | NRIMD | /share/singularity/images/ccs/conda/lcc-conda-4-rocky8.sinf | singularity run --app NRIMD /share/singularity/images/ccs/conda/lcc-conda-4-rocky8.sinf cp -R /usr/local/NRI-MD . cd NRI-MD singularity run --app NRIMD /share/singularity/images/ccs/conda/lcc-conda-4-rocky8.sinf python3 convert_dataset.py |
| MitoHiFi | /share/singularity/images/ccs/MitoHiFi/MitoHiFi.sinf | singularity exec /share/singularity/images/ccs/MitoHiFi/MitoHiFi.sinf findMitoReference.py singularity exec /share/singularity/images/ccs/MitoHiFi/MitoHiFi.sinf mitohifi.py | |
| agat-1.0.0 | agat100 | /share/singularity/images/ccs/conda/lcc-conda-5-rocky8.sinf | singularity run --app agat100 /share/singularity/images/ccs/conda/lcc-conda-5-rocky8.sinf agat |
| mothur-1.48.0 | mothur1480 | /share/singularity/images/ccs/conda/lcc-conda-5-rocky8.sinf | singularity run --app mothur1480 /share/singularity/images/ccs/conda/lcc-conda-5-rocky8.sinf mothur |
| clust-1.17.0 | clust1170 | share/singularity/images/ccs/conda/lcc-conda-6-rocky8.sinf | singularity run --app clust1170 /share/singularity/images/ccs/conda/lcc-conda-6-rocky8.sinf clust |
| clust-1.8.10 | clust1810 | share/singularity/images/ccs/conda/lcc-conda-6-rocky8.sinf | singularity run --app clust1810 /share/singularity/images/ccs/conda/lcc-conda-6-rocky8.sinf clust |
| snap-2013_11_29 | snap20131129 | /share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinf | singularity run --app snap20131129 /share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinf snap |
| kat-2.4.2 | kat242 | /share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinf | singularity run --app kat242 /share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinf kat |
| bowtie2-2.5.1 | bowtie2251 | /share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinf | singularity run --app bowtie2251 /share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinf bowtie2 |
| busco-5.4.6 | busco546 | /share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinf | singularity run --app busco546 /share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinf busco |
| megan-6.24.20 | megan62420 | /share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinf | singularity run --app megan62420 /share/singularity/images/ccs/conda/lcc-conda-7-rocky8.sinf daa-meganizer |
| trim-galore-0.6.10 | trimgalore0610 | /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf | singularity run --app trimgalore0610 /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf trim_galore |
| bsbolt-1.4.8 | bsbolt148 | /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf | singularity run --app bsbolt148 /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf bsbolt |
| qiime2-amplicon-2023.9 | qiime2amplicon20239 | /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf | singularity run --app qiime2amplicon20239 /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf qiime |
| qiime2-shotgun-2023.9 | qiime2shotgun20239 | /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf | singularity run --app qiime2shotgun20239 /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf qiime |
| qiime2-tiny-2023.9 | qiime2tiny20239 | /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf | singularity run --app qiime2tiny20239 /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf qiime |
| deepvariant-1.6 | deepvariant | /share/singularity/images/ccs/deepvariant/ccs-deepvariant-ubuntu2004.sif | singularity run -e --nv /share/singularity/images/ccs/deepvariant/ccs-deepvariant-ubuntu2004.sif /opt/deepvariant/bin/run_deepvariant |
| moose-2023-11-08 | moose | /share/singularity/images/ccs/moose/ccs-moose-rocky8.sif | #Build MOOSE test app #Run MOOSE test app |
| dorado-0.5.3 | doardo053 | /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf | singularity run --app dorado053 /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf dorado |
| pbtk-3.1.1 | pbtk311 | /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf | singularity run --app pbtk311 /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf bam2fastq |
| minimap2-2.28 | minimap2228 | /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf | singularity run --app minimap2228 /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf minimap2 |
| qiime2-amplicon-2024.2 | qiime2amplicon20242 | /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf | singularity run --app qiime2amplicon20242 /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf qiime |
| qiime2-shotgun-2024.2 | qiime2shotgun20242 | /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf | singularity run --app qiime2shotgun20242 /share/singularity/images/ccs/conda/lcc-conda-8-rocky8.sinf qiime |
| GLnexus-1.4.1-3 | glnexus1413 | /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf | singularity run --app glnexus1413 /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf glnexus_cli |
| fastp-0.23.4-3 | fastp02343 | /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf | singularity run --app fastp02343 /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf fastp |
| beast2-2.6.3-2 (with beagle-lib 4.0.0) | beast22632 | /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf | singularity run --app beast22632 /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf beast -beagle_info |
| Dsuite-0.5-r57 | Dsuite05r57 | /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf | singularity run --app Dsuite05r57 /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf Dsuite -h |
| Angsd v0.940 | angsd0940 | /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf | singularity run --app angsd0940 /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf angsd --help |
| PartitionFinder v2.1.1 | PartitionFinder211 | /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf | singularity run --app PartitionFinder211 /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf python /usr/local/Miniconda3/envs/PartitionFinder-211/partitionfinder-2.1.1/PartitionFinder.py -h |
| phyml v3.3.20220408 | phyml3320220408 | /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf | singularity run --app phyml3320220408 /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf phyml -h |
| ngsDist v1.0.10 | ngsdist1010 | /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf | singularity run --app ngsdist1010 /share/singularity/images/ccs/conda/lcc-conda-9-rocky8.sinf /usr/local/ngsDist/ngsDist |
| ciao v4.16 | ciao416 | /share/singularity/images/ccs/ciao/ciao-416.sinf | singularity run --app ciao416 /share/singularity/images/ccs/ciao/ciao-416.sinf ciaover -v |
| PyTorch 2.3.0 / CUDA 12.4 | /share/singularity/images/ccs/pytorch/pytorch-24.04-py3.sinf | singularity exec --nv /share/singularity/images/ccs/pytorch/pytorch-24.04-py3.sinf python | |
| PyTorch 2.2.0 / CUDA 12.3.2 | /share/singularity/images/ccs/pytorch/pytorch-24.01-py3.sinf | singularity exec --nv /share/singularity/images/ccs/pytorch/pytorch-24.01-py3.sinf python | |
| Tassel v5.2.89 | tassel5289 | /share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinf | singularity run --app tassel5289 /share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinf start_tassel.pl -Xmx4g |
| GBS-SNP-CROP v4.1 | gbssnpcrop41 | /share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinf | singularity run --app gbssnpcrop41 /share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinf perl /usr/local/GBS-SNP-CROP-v.4.1/GBS-SNP-CROP-scripts/v.4.1/GBS-SNP-CROP-1.pl |
| samtools 1.20 | samtools120 | /share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinf | singularity run --app samtools120 /share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinf samtools Can also execute with "samtools-1.20 samtools" |
| bcftools 1.20 | bcftools120 | /share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinf | singularity run --app bcftools120 /share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinf bcftools Can also execute with "bcftools-1.20 bcftools" |
| beast2-2.7.7 (with beagle-lib 4.0.1) | beast2277 | /share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinf | singularity run --app beast2277 /share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinf beast singularity run --app beast2277 /share/singularity/images/ccs/conda/lcc-conda-10-rocky8.sinf packagemanager |
| lightning v2.3.1(with timm v1.0.7 and python-dotenv1.01) | /share/singularity/images/ccs/pytorch/pytorch-24.04-py3.sinf | singularity exec --nv /share/singularity/images/ccs/pytorch/pytorch-24.04-py3.sinf python -c "import sys, torch, lightning as L, timm, pkg_resources; print(f'Python version: {sys.version}'); print(f'PyTorch version: {torch.__version__}'); print(f'Lightning version: {L.__version__}'); print(f'timm version: {timm.__version__}'); print(f'python-dotenv version: {pkg_resources.get_distribution(\"python-dotenv\").version}')" | |
| R-plm_1.65 | rplm165 | /share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinf | module load ccs/singularity-3.8.2 singularity run --app rplm165 /share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinf R |
| CmdStanR 0.5.2 and OpenCL | /share/singularity/images/ccs/cmdstanr/lcc-cmdstanr-opencl.sinf | singularity exec --overlay=$OVERLAY --nv /share/singularity/images/ccs/cmdstanr/lcc-cmdstanr-opencl.sinf Rscript example.R | |
| nginx-1.25.3 | nginx1253 | /share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinf | module load ccs/singularity-3.8.2 singularity run --app nginx1253 /share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinf nginx |
| ird-2.0.4.2 | idr202 | /share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinf | module load ccs/singularity-3.8.2 singularity run --app idr2042 /share/singularity/images/ccs/conda/lcc-conda-11-rocky9.sinf idr --help |
How to Run Containerized Programs
There are two ways to run containerized programs: 1) Interactively, or 2) Via a SLURM job submission script. The first method provides a way to check the environment and testing program configuration/options, but is not meant for a full production run as it will take up resources in the login nodes. When you are ready to run the job in the compute nodes, you can do method #2 below.
1) To run a software package installed in the conda container interactively:
1. Load singularity module
| [user@login001]$ module load ccs/singularity |
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2. Invoke the singularity container shell.
[user@login001]$ singularity shell /share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf |
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3. Activate the conda environment for whichever package you want to use, eg samtools-1.10 (the conda package name to be used for interactive use is from column 1 from the above table)
| Singularity lcc-conda-1-centos8.sinf :~> . activate samtools-1.10 |
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4. Then use the package as intended
| (samtools-1.10) Singularity lcc-conda-1-centos8.sinf :~> samtools --version samtools 1.10 Using htslib 1.10.2 Copyright (C) 2019 Genome Research Ltd. |
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5. After usage of that conda package
| (samtools-1.10) Singularity lcc-conda-1-centos8.sinf :~> conda deactivate |
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6. Exit the singularity container
| Singularity lcc-conda-1-centos8.sinf :~> exit |
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2) To run a software package installed in the conda container in a SLURM job submission script.:
For eg. samtools-1.10 (The app name to be used for conda package is from the table above (column 2))
#!/bin/bash #SBATCH -t 00:05:00 #Time for the job to run #SBATCH -n 1 #Number of cores needed for the job; cannot be more than the number of cores available on a single node #SBATCH --mail-type ALL #Send email on start/end #SBATCH --account=col_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 " #Samtools program execution command singularity run --app samtools110 /share/singularity/images/ccs/conda/lcc-conda-1-centos8.sinf samtools --version |
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This example is available in the folder /share/examples/LCC/conda
Center for Computational Sciences