Conda and Containers on LCC
Software listings on this page are no longer maintained.
The authoritative source for software available on LCC is the Software Documentation Service (SDS).
Use SDS to search for available software, containers, and versions: Software Documentation Service (SDS).
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 |
|---|
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 |
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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 |
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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 |
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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 |
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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 |
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soapdenovo-2.40 | soapdenovo240 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf |
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trinity2110 | trinity-2.11.0 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf |
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fast5-0.6.5 | fast5065 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf |
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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 |
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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 |
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mrbayes-3.2.7 | mrbayes327 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf |
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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 |
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pcre-8.44 | pcre844 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf |
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plink-1.90b6.12 | plink190b612 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf |
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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 |
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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 |
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star-2.7.5c | star275c | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf |
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tophat-2.1.1 | tophat211 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf |
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vcftools-0.1.16 | vcftools0116 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf |
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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 |
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fastqc-0.11.9 | fastqc0119 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf |
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blast-2.10.1 | blast2101 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf |
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bowtie-2.4.1 | bowtie241 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf |
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bwa-0.7.17 | bwa0717 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf |
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bedtools-2.29.2 | bedtools2292 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf |
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cdhit-4.6.1 | cdhit461 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf |
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mcl-14.137 | mcl14137 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf |
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mafft-7.471 | mafft7471 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf |
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guidance-2.0 | guidance202 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf |
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raxml-8.2.12 | raxml8212 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf |
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bismark-0.22.3 | bismark0223 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf |
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gatk-4.1.8.1 | gatk4181 | /share/singularity/images/ccs/conda/lcc-conda-2-centos8.sinf |
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exonerate-gff3 | exonerategff3 | /share/singularity/images/ccs/conda/lcc-bio-1-centos8.sinf |
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implicit-landuse | implicitlanduse | /share/singularity/images/ccs/conda/lcc-conda-4-centos8.sinf |
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gdal-3.1.2 | gdal312 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf |
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bayescan-2.0.1 | bayescan201 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf |
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bcftools-1.10.2 | bcftools1102 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf |
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notebook-6.1.4 (includes pandas,numpy,scikit-learn) | notebook614 | /share/singularity/images/ccs/conda/lcc-conda-4-centos8.sinf |
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mdanalysis-1.0.0 | mdanalysis | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf |
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ensembl-vep-101.0 | ensemblvep1010 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf |
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mothur-1.44.3 | mothur1443 | /share/singularity/images/ccs/conda/lcc-bio-1-centos7.sinf |
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mothur-1.44.11 | mothur14411 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf |
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openbabel-2.4.1 | openbabel241 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf |
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structure-2.3.4 | structure234 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf |
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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 |
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minigraph | minigraph | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf |
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annoy-1.17.0 | annoy1170 | /share/singularity/images/ccs/conda/lcc-conda-3-centos8.sinf |
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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 |
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transdecoder-5.5.0 | transdecoder550 | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf |
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transrate-tools-1.0.0 | transratetools100 | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf |
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transrate-1.0.3 | transrate103 | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf |
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detonate-1.11 | detonate111 | /share/singularity/images/ccs/conda/lcc-conda-5-centos8.sinf |
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SPlisHSPlasH | SPlisHSPlasH | /share/singularity/images/ccs/splishsplash/SPlisHSPlasH.sinf |
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cd-hit-4.8.1 |