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  • HPC conda3 software environments

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module load anaconda3
conda-env list

On 1-Mar-2021, the only conda3 environments available are: abyss , admixtools , admixture , angsd , assembly-scan , assembly-stats , astral , augustus , bamm , bamtools , bayescan , bazel , bcftools , beast , beast2 , bedtools , biopython , bismark , blast , boost , bowtie2 , busco , bwa , cairocffi , canu , cap3 , cdhit , checkm-genome , cloog , corset , coverm , cufflinks , cutadapt , dadi , das_tool , diamond , dlcpar , dmd , drep , emboss , enrichm , exonerate , fasta3 , fastai , fastme , fastp , fastqc , faststructure , fastx , ffmpeg , flye , freebayes , freexl , gatk , gatk4 , gblocks , gdal , gdc , glpk , gmap , gmsh , gnuplot , google-sparsehash , googlesparsehash , gradle , graftm , graftm_genome , graphbin , gtdbtk , hdf4 , hdf5 , hisat2 , hmmer , hmmer2 , iqtree , iqtree1 , itsx , jags , jellyfish , julia , kraken , kraken2 , krona , lastz , libnetcdf , mafft , mapdamage2 , maxbin2 , mcl , medaka , megahit , metabat2 , metawrap-mg , metis , mfqe , migrate , minimap2 , mirdeep2 , mrbayes , multiqc , muscle , netcdf-fortran , netcdf4 , nettle , newick_utils , nlopt , orfm , orthofinder , pal2nal , paml , pandoc , parallel , pcre , pcre2 , pear , petsc , phyluce-1.7.0 , picard , pipits , plink , pplacer , prodigal , proj4 , proteinortho , purge_haplotigs , pyfastx , pyproj , qgis , qualimap , quast , R-36 , R-403 , r-rstan , raxml , rcorrector , rdpclassifier , repeatmodeler , rsem , ruby , salmon , samtools , scalpel , seqtk , sga , shannon , shovill , slim , sortmerna , spades , sparsehash , sratools , stacks , star , stringtie , structure , tophat , tpp , transdecoder , transrate , treemix , treeshrink , trimal , trimgalore , trimmomatic , trinity , trinotate , vcflib , vcftools , velvet , vsearch

Generally speaking, HPC staff are not familiar with using software installed on the HPC cluster.  However, we may be able to provide general assistance with running software when requested.  

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