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list-of-software [2019/01/25 11:29]
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list-of-software [2020/08/09 13:05] (current)
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 In general you can use the command ''module avail'' to show you the list of available software and their versions. Sometimes there are other software packages installed which aren't listed via the modules system; if you're curious you can look around in ///export/apps// to see if you can find what you're looking for. In general you can use the command ''module avail'' to show you the list of available software and their versions. Sometimes there are other software packages installed which aren't listed via the modules system; if you're curious you can look around in ///export/apps// to see if you can find what you're looking for.
  
-Otherwise, here is a feeble attempt to list the software we have installed at ILRI, their versions, and (possibly) anyone who has experience running it. We will attempt to keep this list updated as the One True List™.+Otherwise, here is a feeble attempt to list the software we have installed at ILRI, their versions, and (possibly) anyone who has experience running it. We endeavor to keep this list updated as the One True List™.
  
 ^Name           ^Latest version                ^How to load                 ^Contact   ^ ^Name           ^Latest version                ^How to load                 ^Contact   ^
 |[[abyss-software|abyss]]|2.1.4|''module load abyss/2.1.4''| | |[[abyss-software|abyss]]|2.1.4|''module load abyss/2.1.4''| |
 |abacas|1.3.1|''module load abacas/1.3.1''| | |abacas|1.3.1|''module load abacas/1.3.1''| |
 +|[[ace-software|ace]]|1.01|''module load ace/1.01''| |
 |[[ACT-software|ACT]]|13.0.0|''module load act/13.0.0''| | |[[ACT-software|ACT]]|13.0.0|''module load act/13.0.0''| |
 |[[admixture-software|admixture]]|1.3.0|''module load admixture/1.3.0''| | |[[admixture-software|admixture]]|1.3.0|''module load admixture/1.3.0''| |
Line 21: Line 22:
 |[[artemis-software|artemis]]|16.0.0|''module load act/16.0.0''| | |[[artemis-software|artemis]]|16.0.0|''module load act/16.0.0''| |
 |[[augustus-software|augustus]]|3.3|''module load augustus/3.3''| | |[[augustus-software|augustus]]|3.3|''module load augustus/3.3''| |
 +|[[awscli-software|awscli]]|1.17.9|''module load awscli/1.17.9''| |
 |[[bam-readcount-software|bam-readcount]]|0.8.0|''module load bam-readcount/0.8.0''| | |[[bam-readcount-software|bam-readcount]]|0.8.0|''module load bam-readcount/0.8.0''| |
 |[[bamtools-software|bamtools]]|2.5.1|''module load bamtools/2.5.1''| | |[[bamtools-software|bamtools]]|2.5.1|''module load bamtools/2.5.1''| |
 +|[[barrnap-software|barrnap]]|0.9|''module load barrnap/0.9''| |
 |bayescan|2.1|''module load bayescan/2.1''| | |bayescan|2.1|''module load bayescan/2.1''| |
 +|[[bbmap-software|bbmap]]|38.67|''module load bbmap/38.67''| |
 |[[bcftools-software|bcftools]]|1.8|''module load bcftools/1.8''| | |[[bcftools-software|bcftools]]|1.8|''module load bcftools/1.8''| |
-|[[beagle-software|beagle]]|3.0.2|''module load beagle/3.0.2''| | +|[[beagle-software|beagle]]|3.1.2|''module load beagle/3.1.2''| | 
-|[[beast-software|beast]]|1.10.2|''module load beast/1.10.2''| |+|[[beast-software|beast]]|1.10.4|''module load beast/1.10.4''| |
 |[[bedops-software|bedops]]|2.4.29|''module load bedops/2.4.29''| | |[[bedops-software|bedops]]|2.4.29|''module load bedops/2.4.29''| |
-|[[bedtools-software|bedtools]]|2.25.0|''module load bedtools/2.25.0''| |+|[[bedtools-software|bedtools]]|2.29.0|''module load bedtools/2.29.0''| |
 |[[binpacker-software|binpacker]]|1.0|''module load binpacker/1.0''| | |[[binpacker-software|binpacker]]|1.0|''module load binpacker/1.0''| |
 |[[bioperl-software|bioperl]]|1.7.2|''module load bioperl/1.7.2''| | |[[bioperl-software|bioperl]]|1.7.2|''module load bioperl/1.7.2''| |
 |[[bitseq-software|bitseq]]|0.7.5|''module load bitseq/0.7.5''| | |[[bitseq-software|bitseq]]|0.7.5|''module load bitseq/0.7.5''| |
 |[[blasr-software|blasr]]|smrtanalysis-4.0.0|''module load blasr/smrtanalysis-4.0.0''| | |[[blasr-software|blasr]]|smrtanalysis-4.0.0|''module load blasr/smrtanalysis-4.0.0''| |
-|[[blast-software|blast]]|2.6.0+|''module load blast/2.6.0+''| |+|[[blast-software|blast]]|2.10.0+|''module load blast/2.10.0+''| |
 |[[blobtools-software|blobtools]]|0.9.19.3|''module load blobtools/0.9.19.3''| | |[[blobtools-software|blobtools]]|0.9.19.3|''module load blobtools/0.9.19.3''| |
 |blat|06-Aug-2013|''module load blat/06-Aug-2013''| | |blat|06-Aug-2013|''module load blat/06-Aug-2013''| |
-|[[bowtie-software|bowtie1 ]]|1.1.1|''module load bowtie/1.1.1''| |+|[[bowtie-software|bowtie1 ]]|1.2.3|''module load bowtie/1.2.3''| |
 |[[bowtie2-software|bowtie2 ]]|2.3.4.1|''module load bowtie2/2.3.4.1''| | |[[bowtie2-software|bowtie2 ]]|2.3.4.1|''module load bowtie2/2.3.4.1''| |
 |[[brig-software|brig]]|0.95|''module load brig/0.95''| | |[[brig-software|brig]]|0.95|''module load brig/0.95''| |
-|[[busco-software|BUSCO ]]|3.0.2|''module load BUSCO/3.0.2''| | +|[[busco-software|BUSCO ]]|4.0.6|''module load BUSCO/4.0.6''| | 
-|[[bwa-software|bwa]]|0.7.15|''module load bwa/0.7.15''| |+|[[bwa-software|bwa]]|0.7.17|''module load bwa/0.7.17''| |
 |[[cafe-software|cafe]]|4.1|''module load cafe/4.1''| | |[[cafe-software|cafe]]|4.1|''module load cafe/4.1''| |
 |cangs|1.1|''module load cangs/1.1''| | |cangs|1.1|''module load cangs/1.1''| |
Line 49: Line 53:
 |celera-wgs|6.1|''module load celera-wgs/6.1''| | |celera-wgs|6.1|''module load celera-wgs/6.1''| |
 |censor|4.2.28|''module load censor/4.2.28''| | |censor|4.2.28|''module load censor/4.2.28''| |
-|[[changeo-software|changeo]]|0.3.9|''module load changeo/0.3.9''| | +|[[changeo-software|changeo]]|1.0.0|''module load changeo/1.0.0''| | 
-|[[circos-software|circos]]|0.67|''module load circos/0.67''| |+|[[checkm-software|checkm]]|1.1.2|''module load checkm/1.1.2''| | 
 +|[[circos-software|circos]]|0.69-9|''module load circos/0.69-9''| |
 |[[clonalframe-software|clonalframe]]|1.2|''module load clonalframe/1.2''| | |[[clonalframe-software|clonalframe]]|1.2|''module load clonalframe/1.2''| |
 |[[clonalframeml-software|clonalframeml]]|1.0|''module load clonalframeml/1.0''| | |[[clonalframeml-software|clonalframeml]]|1.0|''module load clonalframeml/1.0''| |
Line 64: Line 69:
 |dendroscope|2.7.4|''module load dendroscope/2.7.4''| | |dendroscope|2.7.4|''module load dendroscope/2.7.4''| |
 |[[diamond-software|diamond]]|0.9.9|''module load diamond/0.9.9''| | |[[diamond-software|diamond]]|0.9.9|''module load diamond/0.9.9''| |
 +|[[drep-software|drep]]|2.5.4|''module load drep/2.5.4''| |
 |[[ea-utils-software|ea-utils]]|1.04.807|''module load ea-utils/1.04.807''| | |[[ea-utils-software|ea-utils]]|1.04.807|''module load ea-utils/1.04.807''| |
 |[[edirect-software|edirect]]| 7.80 | ''module load edirect/7.80'' | | |[[edirect-software|edirect]]| 7.80 | ''module load edirect/7.80'' | |
Line 72: Line 78:
 |[[exabayes-software|exabayes]]|1.4.1|''module load exabayes/1.4.1''| | |[[exabayes-software|exabayes]]|1.4.1|''module load exabayes/1.4.1''| |
 |[[express-software|express]]|1.5.1|''module load express/1.5.1''| | |[[express-software|express]]|1.5.1|''module load express/1.5.1''| |
 +|[[fastANI-software|fastANI]]|1.3|''module load fastANI/1.3''| |
 |[[fastPHASE-software|fastPHASE]]|1.4.8|''module load fastPHASE/1.4.8''| | |[[fastPHASE-software|fastPHASE]]|1.4.8|''module load fastPHASE/1.4.8''| |
 |[[fastqc-software|fastqc]]|0.11.7|''module load fastqc/0.11.7''| | |[[fastqc-software|fastqc]]|0.11.7|''module load fastqc/0.11.7''| |
 |[[faststructure-software|fastSTRUCTURE]]|1.0|''module load fastSTRUCTURE/1.0''| | |[[faststructure-software|fastSTRUCTURE]]|1.0|''module load fastSTRUCTURE/1.0''| |
 +|[[fasttree-software|fasttree]]|2.1.11|''module load fasttree/2.1.11''| |
 |[[fastx-toolkit-software|fastx_toolkit]]|0.0.13|''module load fastx_toolkit/0.0.13''| | |[[fastx-toolkit-software|fastx_toolkit]]|0.0.13|''module load fastx_toolkit/0.0.13''| |
 |figtree|1.4.0|''module load figtree/1.4.0''| | |figtree|1.4.0|''module load figtree/1.4.0''| |
Line 82: Line 90:
 |[[flexbar-software|flexbar]]|2.7.0|''module load flexbar/2.7.8''| | |[[flexbar-software|flexbar]]|2.7.0|''module load flexbar/2.7.8''| |
 |[[flux-capacitor-software|flux-capacitor]]|1.6.1|''module load flux-capacitor/1.6.1''| | |[[flux-capacitor-software|flux-capacitor]]|1.6.1|''module load flux-capacitor/1.6.1''| |
 +|[[flye-software|flye]]|2.4.2|''module load flye/2.4.2''| |
 |frappe|1.1|''module load frappe/1.1''| | |frappe|1.1|''module load frappe/1.1''| |
-|[[fraggenescan-software|FragGeneScan ]]|1.19|''module load fraggenescan/1.19''| |+|[[fraggenescan-software|FragGeneScan ]]|1.30|''module load fraggenescan/1.30''| |
 |[[freebayes-software|FreeBayes ]]|1.0.2|''module load freebayes/1.0.2''| | |[[freebayes-software|FreeBayes ]]|1.0.2|''module load freebayes/1.0.2''| |
 |[[gassflow-software|GassFlow ]]|1.0|''module load gassflow/1.0''| | |[[gassflow-software|GassFlow ]]|1.0|''module load gassflow/1.0''| |
Line 99: Line 108:
 |[[groovy-software|groovy]]|2.4.9|''module load groovy/2.4.9''| | |[[groovy-software|groovy]]|2.4.9|''module load groovy/2.4.9''| |
 |[[gsea-software|GSEA]]|2.2.3|''module load gsea/2.2.3''| | |[[gsea-software|GSEA]]|2.2.3|''module load gsea/2.2.3''| |
 +|[[gtdbtk-software|gtdbtk]]|1.1.1|''module load gtdbtk/1.1.1''| |
 |[[guidance-software|guidance]]|2.02|''module load guidance/2.02''| | |[[guidance-software|guidance]]|2.02|''module load guidance/2.02''| |
 |[[hapflk-software|hapflk]]|1.4|''module load hapflk/1.4''| | |[[hapflk-software|hapflk]]|1.4|''module load hapflk/1.4''| |
 |hapmix|2.0|''module load hapmix/2.0''| | |hapmix|2.0|''module load hapmix/2.0''| |
 |[[hdf5-software|hdf5]]|1.8.19|''module load hdf5/1.8.19''| | |[[hdf5-software|hdf5]]|1.8.19|''module load hdf5/1.8.19''| |
-|[[hmmer-software|hmmer]]|3.1b2|''module load hmmer/3.1b2''| |+|[[hmmer-software|hmmer]]|3.3|''module load hmmer/3.3''| |
 |[[hpg-variant-software|hpg-variant]]|1.0|''module load hpg-variant/1.0''| | |[[hpg-variant-software|hpg-variant]]|1.0|''module load hpg-variant/1.0''| |
 |[[hisat2-software|hisat2]]|2.1.0|''module load hisat2/2.1.0''| | |[[hisat2-software|hisat2]]|2.1.0|''module load hisat2/2.1.0''| |
-|[[htseq-software|htseq]]|0.6.1|''module load htseq/0.6.1''| | +|[[htseq-software|htseq]]|0.9.1|''module load htseq/0.9.1''| | 
-|[[htslib-software|htslib]]|1.8|''module load htslib/1.8''| | +|[[htslib-software|htslib]]|1.9|''module load htslib/1.9''| | 
-|[[igblast-software|igblast]]|1.6.0|''module load igblast/1.6.0''| |+|[[idba-software|idba]]|1.1.2|''module load idba/1.1.2''| | 
 +|[[igblast-software|igblast]]|1.10.0|''module load igblast/1.10.0''| | 
 +|[[igdiscover-software|igdiscover]]|0.12.3|''module load igdiscover/0.12.3''| |
 |[[igrec-software|igrec]]|3.0.0|''module load igrec/3.0.0''| | |[[igrec-software|igrec]]|3.0.0|''module load igrec/3.0.0''| |
 +|[[igsimulator-software|igsimulator]]|git-c3778b74|''module load igsimulator/git-c3778b74''| |
 +|[[igtree-software|iqtree]]|1.6.12|''module load iqtree/1.6.12''| |
 |[[igv-software|igv]]|2.4.5|''module load igv/2.4.5''| | |[[igv-software|igv]]|2.4.5|''module load igv/2.4.5''| |
 |[[igvtools-software|igvtools]]|2.3.98|''module load igvtools/2.3.98''| | |[[igvtools-software|igvtools]]|2.3.98|''module load igvtools/2.3.98''| |
 +|[[infernal-software|infernal]]|1.1.2|''module load infernal/1.1.2''| |
 |[[interproscan-software|interproscan]]|5.13|''module load interproscan/5.13''| | |[[interproscan-software|interproscan]]|5.13|''module load interproscan/5.13''| |
 |i-tasser|latest|''module load i-tasser/latest''| | |i-tasser|latest|''module load i-tasser/latest''| |
Line 119: Line 134:
 |[[kaiju-software|kaiju]]|1.4.4|''module load kaiju/1.4.4''| | |[[kaiju-software|kaiju]]|1.4.4|''module load kaiju/1.4.4''| |
 |[[kallisto-software|kallisto]]|0.43.0|''module load kallisto/0.43.0''| | |[[kallisto-software|kallisto]]|0.43.0|''module load kallisto/0.43.0''| |
 +|[[karect-software|karect]]|1.0|''module load karect/1.0''| |
 |[[kat-software|kat]]|2.3.4|''module load kat/2.3.4''| | |[[kat-software|kat]]|2.3.4|''module load kat/2.3.4''| |
 |[[kmc-software|kmc]]|3.0.0|''module load kmc/3.0.0''| | |[[kmc-software|kmc]]|3.0.0|''module load kmc/3.0.0''| |
 |[[kmergenie-software|kmergenie]]|1.7038|''module load kmergenie/1.7038''| | |[[kmergenie-software|kmergenie]]|1.7038|''module load kmergenie/1.7038''| |
 |[[kmer-ssr-software|kmer-ssr]]|git-4043c0e7|''module load kmer-ssr/git-4043c0e7''| | |[[kmer-ssr-software|kmer-ssr]]|git-4043c0e7|''module load kmer-ssr/git-4043c0e7''| |
-|[[kraken-software|kraken]]|0.10.5|''module load kraken/0.10.5''| |+|[[kraken-software|kraken]]|2.0.8-beta|''module load kraken/2.0.8-beta''| |
 |krona|2.4|''module load krona/2.4''| | |krona|2.4|''module load krona/2.4''| |
 |lamp|2.5|''module load lamp/2.5''| | |lamp|2.5|''module load lamp/2.5''| |
Line 129: Line 145:
 |ldhat|2.1|''module load ldhat/2.1''| | |ldhat|2.1|''module load ldhat/2.1''| |
 |[[libsvm-software|libsvm]]|3.20|''module load libsvm/3.20''| | |[[libsvm-software|libsvm]]|3.20|''module load libsvm/3.20''| |
 +|[[lighter-software|lighter]]|1.1.2|''module load lighter/1.1.2''| |
 +|[[lordec-software|lordec]]|0.9|''module load lordec/0.9''| |
 |lucy|1.19p|''module load lucy/1.19p''| | |lucy|1.19p|''module load lucy/1.19p''| |
 |[[mafft-software|mafft]]|7.313|''module load mafft/7.313''| | |[[mafft-software|mafft]]|7.313|''module load mafft/7.313''| |
 |[[mapsplice-software|mapsplice]]|2.2.0|''module load mapsplice/2.2.0''| | |[[mapsplice-software|mapsplice]]|2.2.0|''module load mapsplice/2.2.0''| |
 |[[marginalign-software|marginalign]]|git-2369dafd|''module load marginalign/git-2369dafd''| | |[[marginalign-software|marginalign]]|git-2369dafd|''module load marginalign/git-2369dafd''| |
-|[[mash-software|mash]]|2.0|''module load mash/2.0''| | +|[[marginpolish-software|marginpolish]]|1.0.0|''module load marginpolish/1.0.0''| | 
-|[[masurca-software|masurca]]|3.2.8|''module load masurca/3.2.8''| |+|[[mash-software|mash]]|2.2|''module load mash/2.2''| | 
 +|[[masurca-software|masurca]]|3.3.1|''module load masurca/3.3.1''| |
 |mauve|2.3.1|''module load mauve/2.3.1''| | |mauve|2.3.1|''module load mauve/2.3.1''| |
 +|[[maxbin2-software|maxbin2]]|2.2.7|''module load maxbin2/2.2.7''| |
 |maximus|0.2|''module load maximus/0.2''| | |maximus|0.2|''module load maximus/0.2''| |
 |[[mcl-software|mcl]]|14-137|''module load mcl/14-137''| | |[[mcl-software|mcl]]|14-137|''module load mcl/14-137''| |
 |[[mecat-software|MECAT]]|git-d04bfa84|''module load MECAT/git-d04bfa84''| | |[[mecat-software|MECAT]]|git-d04bfa84|''module load MECAT/git-d04bfa84''| |
 +|[[medaka-software|medaka]]|0.8.2|''module load medaka/0.8.2''| |
 |[[megahit-software|megahit]]|1.1.4|''module load megahit/1.1.4''| | |[[megahit-software|megahit]]|1.1.4|''module load megahit/1.1.4''| |
 |megan|4.70.4|''module load megan/4.70.4''| | |megan|4.70.4|''module load megan/4.70.4''| |
 +|[[megax-software|megax]]|10.0.5|''module load megax/10.0.5''| |
 |[[metabat-software|metabat]]|2.12.1|''module load metabat/2.12.1''| | |[[metabat-software|metabat]]|2.12.1|''module load metabat/2.12.1''| |
 +|[[metaphlan2-software|metaphlan2]]|2.9.5|''module load metaphlan2/2.9.5''| |
 |[[metis-software|metis]]|5.1.0|''module load metis/5.1.0''| | |[[metis-software|metis]]|5.1.0|''module load metis/5.1.0''| |
 |[[migec-software|migec]]|1.2.4a|''module load migec/1.2.4a''| | |[[migec-software|migec]]|1.2.4a|''module load migec/1.2.4a''| |
Line 148: Line 171:
 |[[minimap2-software|minimap2]]|2.13|''module load minimap2/2.13''| | |[[minimap2-software|minimap2]]|2.13|''module load minimap2/2.13''| |
 |[[minpath-software|MinPath]]|1.0.2|''module load MinPath/1.2''| | |[[minpath-software|MinPath]]|1.0.2|''module load MinPath/1.2''| |
-|[[mira-software#v4.0.2|mira ]]|4.0.2|''module load mira/4.0.2''| |+|[[mira-software#v4.0.2|mira]]|4.0.2|''module load mira/4.0.2''| | 
 +|[[mirdeep2-software|mirdeep2]]|0.1.3|''module load mirdeep2/0.1.3''| |
 |[[mitools-software|mitools]]|1.4|''module load mitools/1.4''| | |[[mitools-software|mitools]]|1.4|''module load mitools/1.4''| |
-|[[mixcr-software|mixcr]]|2.0.1|''module load mixcr/2.0.1''| |+|[[mixcr-software|mixcr]]|3.0.11|''module load mixcr/3.0.11''| |
 |mkatari-ilri|latest|''module load mkatari-ilri/latest''| | |mkatari-ilri|latest|''module load mkatari-ilri/latest''| |
 |[[modeller-software|modeller]]|9.17|''module load modeller/9.17''| | |[[modeller-software|modeller]]|9.17|''module load modeller/9.17''| |
-|[[mothur-software|mothur]]|1.39.5|''module load mothur/1.39.5''| |+|[[mothur-software|mothur]]|1.44.1|''module load mothur/1.44.1''| |
 |[[mothur-krona-software|mothur-krona]]|git-87499a0|''module load mothur-krona/git-87499a0''| | |[[mothur-krona-software|mothur-krona]]|git-87499a0|''module load mothur-krona/git-87499a0''| |
 |mpiblast|1.6.0|''module load mpiblast/1.6.0''| | |mpiblast|1.6.0|''module load mpiblast/1.6.0''| |
 |mrbayes|3.2.2|''module load mrbayes/3.2.2''| | |mrbayes|3.2.2|''module load mrbayes/3.2.2''| |
 |[[multiqc-software|multiqc]]|1.4|''module load multiqc/1.4''| | |[[multiqc-software|multiqc]]|1.4|''module load multiqc/1.4''| |
-|[[muscle-software|muscle]]|3.8.31|''module load muscle/3.8.31'' |+|[[muscle-software|muscle]]|3.8.1551|''module load muscle/3.8.1551'' |
 |[[mummer-software|MUMmer]]|3.23|''module load MUMmer/3.23''| | |[[mummer-software|MUMmer]]|3.23|''module load MUMmer/3.23''| |
 |[[nanopolish-software|nanopolish]]|0.10.2|''module load nanopolish/0.10.2''| | |[[nanopolish-software|nanopolish]]|0.10.2|''module load nanopolish/0.10.2''| |
 |[[netmhcpan-software|netmhcpan]]|2.8|''module load netmhcpan/2.8''| | |[[netmhcpan-software|netmhcpan]]|2.8|''module load netmhcpan/2.8''| |
 |[[nextclip-software|nextclip]]|1.3.1|''module load nextclip/1.3.1''| | |[[nextclip-software|nextclip]]|1.3.1|''module load nextclip/1.3.1''| |
 +|[[nextflow-software|nextflow]]|20.04.1|''module load nextflow/20.04.1''| |
 |[[ntcard-software|ntCard]]|1.0.0|''module load ntCard/1.0.0''| | |[[ntcard-software|ntCard]]|1.0.0|''module load ntCard/1.0.0''| |
 |[[ngsqctoolkit-software|ngsqctoolkit]]|2.3.3|''module load ngsqctoolkit/2.3.3''| | |[[ngsqctoolkit-software|ngsqctoolkit]]|2.3.3|''module load ngsqctoolkit/2.3.3''| |
 |novacraft|3.02.07|''module load novacraft/3.02.07''| | |novacraft|3.02.07|''module load novacraft/3.02.07''| |
 |[[oases-software|oases]]|0.2.08|''module load oases/0.2.08''| | |[[oases-software|oases]]|0.2.08|''module load oases/0.2.08''| |
-|[[ocaml-software#v4.02.1|ocaml ]]|4.02.1|''module load ocaml/4.02.1''| | +|[[ocaml-software#v4.02.1|ocaml]]|4.02.1|''module load ocaml/4.02.1''| | 
-|[[opam-software#v1.2.0|opam ]]|1.2.0|''module load opam/1.2.0''| |+|[[opam-software#v1.2.0|opam]]|1.2.0|''module load opam/1.2.0''| |
 |orthomcl|2.0.3|''module load orthomcl/2.0.3''| | |orthomcl|2.0.3|''module load orthomcl/2.0.3''| |
 +|[[orp-software|Oyster River Protocol]]|2.2.8|''module load orp/2.2.8''| |
 |[[pagan-software|pagan]]|0.61|''module load pagan/0.61''| | |[[pagan-software|pagan]]|0.61|''module load pagan/0.61''| |
 |[[pairfq-software|pairfq]]|0.14.4|''module load pairfq/0.14.4''| | |[[pairfq-software|pairfq]]|0.14.4|''module load pairfq/0.14.4''| |
Line 175: Line 201:
 |[[pandaseq-software|pandaseq]]|2.8.1|''module load pandaseq/2.8.1'' | |[[pandaseq-software|pandaseq]]|2.8.1|''module load pandaseq/2.8.1'' |
 |[[pasta-software|pasta]]|d939adb2|''module load pasta/d939adb2'' | |[[pasta-software|pasta]]|d939adb2|''module load pasta/d939adb2'' |
-|[[pear-software|pear]]|git-2c309dc|''module load pear/git-2c309dc''| |+|[[pear-software|pear]]|0.9.6|''module load pear/0.9.6''| | 
 +|[[pblat-software|pblat]]|2.1|''module load pblat/2.1''| |
 |[[pbsuite-software|pbsuite]]|15.8.24|''module load pbsuite/15.8.24''| | |[[pbsuite-software|pbsuite]]|15.8.24|''module load pbsuite/15.8.24''| |
-|[[perl-software|perl]]|5.22.3|''module load perl/5.22.3''| |+|[[perl-software|perl]]|5.28.2|''module load perl/5.28.2''| |
 |[[pgdspider-software|PGDSpider]]|2.1.1.0|''module load pgdspider/2.1.1.0''| | |[[pgdspider-software|PGDSpider]]|2.1.1.0|''module load pgdspider/2.1.1.0''| |
 |phrap|1.080812|''module load phrap/1.080812''| | |phrap|1.080812|''module load phrap/1.080812''| |
Line 185: Line 212:
 |[[picard-software|picard]]|2.17.0|''module load picard/2.17.0''| | |[[picard-software|picard]]|2.17.0|''module load picard/2.17.0''| |
 |[[picrust-software#v1.0.0|picrust]]|1.0.0|''module load picrust/1.0.0''| | |[[picrust-software#v1.0.0|picrust]]|1.0.0|''module load picrust/1.0.0''| |
-|[[pilon-software|pilon]]|1.2.2|''module load pilon/1.2.2''| |+|[[pilon-software|pilon]]|1.23|''module load pilon/1.23''| |
 |[[platanus-software|platanus]]|1.2.1|''module load platanus/1.2.1''| | |[[platanus-software|platanus]]|1.2.1|''module load platanus/1.2.1''| |
-|[[plink-software|plink]]|1.9|''module load plink/1.9''| |+|[[plink-software|plink]]|2.00-alpha|''module load plink/2.00-alpha''| |
 |[[polyphen-software|polyphen]]|2.2.2|''module load polyphen/2.2.2''| | |[[polyphen-software|polyphen]]|2.2.2|''module load polyphen/2.2.2''| |
 +|[[porechop-software|porechop]]|0.2.4|''module load porechop/0.2.4''| |
 +|[[pplacer-software|pplacer]]|1.1.alpha19|''module load pplacer/1.1.alpha19''| |
 |[[prank-software|prank]]|170427|''module load prank/170427''| | |[[prank-software|prank]]|170427|''module load prank/170427''| |
-|[[presto-software|presto]]|0.5.3|''module load presto/0.5.3''| |+|[[presto-software|presto]]|0.5.13|''module load presto/0.5.13''| |
 |primer3|2.3.6|''module load primer3/2.3.6''| | |primer3|2.3.6|''module load primer3/2.3.6''| |
-|[[prokka-software|prokka]]|1.11|''module load prokka/1.11''| |+|[[prinseq-software|prinseq]]|0.20.4|''module load prinseq/0.20.4''| | 
 +|[[prodigal-software|prodigal]]|2.6.3|''module load prodigal/2.6.3''| | 
 +|[[prokka-software|prokka]]|1.14.6|''module load prokka/1.14.6''| |
 |[[provean-software|provean]]|1.1.5|''module load provean/1.1.5''| | |[[provean-software|provean]]|1.1.5|''module load provean/1.1.5''| |
-|[[python-software|python]]|3.7.2|''module load python/3.7''| |+|[[python-software|python]]|3.7.7|''module load python/3.7''| |
 |qdd|3_beta|''module load qdd/3_beta''| | |qdd|3_beta|''module load qdd/3_beta''| |
 |[[qiime-software|qiime]]|1.9.1|''module load qiime/1.9.1''| | |[[qiime-software|qiime]]|1.9.1|''module load qiime/1.9.1''| |
-|[[qiime2-software|qiime2]]|2018.6|''module load qiime2/2018.6''| | +|[[qiime2-software|qiime2]]|2019.10|''module load qiime2/2019.10''| | 
-|[[quast-software|quast]]|4.5|''module load quast/4.5''| |+|[[quast-software|quast]]|5.0.2|''module load quast/5.0.2''| | 
 +|[[quickmerge-software|quickmerge]]|0.3|''module load quickmerge/0.3''| |
 |[[quorum-software|Quorum]]|1.1.1|''module load quorum/1.1.1''| | |[[quorum-software|Quorum]]|1.1.1|''module load quorum/1.1.1''| |
-|[[r-software|R]]|3.5.2|''module load R/3.5''| |+|[[r-software|R]]|3.6.1|''module load R/3.6''| |
 |[[racon-software|racon]]|1.3.1|''module load racon/1.3.1''| | |[[racon-software|racon]]|1.3.1|''module load racon/1.3.1''| |
 |[[rmblast-software|rmblast]]|2.2.28|''module load rmblast/2.2.28''| | |[[rmblast-software|rmblast]]|2.2.28|''module load rmblast/2.2.28''| |
-|rapsearch|2.10|''module load rapsearch/2.10''| |+|[[rapsearch-software|rapsearch]]|2.22|''module load rapsearch/2.22''| |
 |[[ratt-software|RATT]]|r18|''module load ratt/r18''| | |[[ratt-software|RATT]]|r18|''module load ratt/r18''| |
 |[[raxml-software|RAxML]]|8.2.12|''module load RAxML/8.2.12''| | |[[raxml-software|RAxML]]|8.2.12|''module load RAxML/8.2.12''| |
Line 209: Line 241:
 |[[rdp-classifier-software|RDP Classifier]]|2.11|''module load rdp-classifier/2.11''| | |[[rdp-classifier-software|RDP Classifier]]|2.11|''module load rdp-classifier/2.11''| |
 |repeatmasker|4.0.5|''module load repeatmasker/4.0.5''| | |repeatmasker|4.0.5|''module load repeatmasker/4.0.5''| |
 +|[[repseqio-software|repseqio]]|1.3.3|''module load repseqio/1.3.3''| |
 |[[root-software|root]]|6.08.06|''module load root/6.08.06''| | |[[root-software|root]]|6.08.06|''module load root/6.08.06''| |
 |[[rrnaselector-software|rRNASelector]]|1.1|''module load rrnaselector/1.1''| | |[[rrnaselector-software|rRNASelector]]|1.1|''module load rrnaselector/1.1''| |
Line 214: Line 247:
 |[[rseqc-software|rseqc]]|2.6.4|''module load rseqc/2.6.4''| | |[[rseqc-software|rseqc]]|2.6.4|''module load rseqc/2.6.4''| |
 |[[ruby-software|ruby]]|2.2.3|''module load ruby/2.2.3''| | |[[ruby-software|ruby]]|2.2.3|''module load ruby/2.2.3''| |
-|[[samtools-software|samtools]]|1.8|''module load samtools/1.8''| |+|[[samtools-software|samtools]]|1.9|''module load samtools/1.9''| |
 |[[sailfish-software|sailfish]]|0.9.2|''module load sailfish/0.9.2''| | |[[sailfish-software|sailfish]]|0.9.2|''module load sailfish/0.9.2''| |
 |[[salmon-software|salmon]]|0.9.1|''module load salmon/0.9.1''| | |[[salmon-software|salmon]]|0.9.1|''module load salmon/0.9.1''| |
 |[[scipio-software|scipio]]|1.4.1|''module load scipio/1.4.1''| | |[[scipio-software|scipio]]|1.4.1|''module load scipio/1.4.1''| |
 |[[scythe-software|scythe]]|0.994-beta|''module load scythe/0.994-beta''| | |[[scythe-software|scythe]]|0.994-beta|''module load scythe/0.994-beta''| |
 +|[[sepp-software|sepp]]|4.3.8|''module load sepp/4.3.8''| |
 |[[seroba-software|seroba]]|1.0.0|''module load seroba/1.0.0''| | |[[seroba-software|seroba]]|1.0.0|''module load seroba/1.0.0''| |
 |seq_crumbs|0.1.8|''module load seq_crumbs/0.1.8''| | |seq_crumbs|0.1.8|''module load seq_crumbs/0.1.8''| |
-|[[seqkit-software|seqkit]]|0.7.2|''module load seqkit/0.7.2''| |+|[[seqkit-software|seqkit]]|0.11.0|''module load seqkit/0.11.0''| |
 |[[seqqs-software|seqqs]]|git-3d053750|''module load seqqs/git-3d053750''| | |[[seqqs-software|seqqs]]|git-3d053750|''module load seqqs/git-3d053750''| |
-|[[seqtk-software|seqtk]]|1.2-r102|''module load seqtk/1.2-r102''| |+|[[seqtk-software|seqtk]]|1.3|''module load seqtk/1.3''| |
 |[[shannon-software|shannon]]|0.0.2|''module load shannon/0.0.2''| | |[[shannon-software|shannon]]|0.0.2|''module load shannon/0.0.2''| |
 +|[[shasta-software|shasta]]|0.4.0|''module load shasta/0.4.0''| |
 |[[sickle-software|sickle]]|1.33|''module load sickle/1.33''| | |[[sickle-software|sickle]]|1.33|''module load sickle/1.33''| |
 |[[sift-software|sift]]|4.0.3b|''module load sift/4.0.3b''| | |[[sift-software|sift]]|4.0.3b|''module load sift/4.0.3b''| |
 |[[sistr-software|sistr]]|1.0.2|''module load sistr/1.0.2''| | |[[sistr-software|sistr]]|1.0.2|''module load sistr/1.0.2''| |
 |[[smalt-software|smalt]]|0.7.6|''module load smalt/0.7.6''| | |[[smalt-software|smalt]]|0.7.6|''module load smalt/0.7.6''| |
 +|[[smartdenovo-software|smartdenovo]]|git-5cc1356b|''module load smartdenovo/git-5cc1356b''| |
 +|[[snakemake-software|snakemake]]|5.7.0|''module load snakemake/5.7.0''| |
 |snowhite|1.1.4|''module load snowhite/1.1.4''| | |snowhite|1.1.4|''module load snowhite/1.1.4''| |
 |[[snpeff-software|SnpEff & SnpSift]]|4.1g|''module load snpeff/4.1g''| | |[[snpeff-software|SnpEff & SnpSift]]|4.1g|''module load snpeff/4.1g''| |
Line 239: Line 276:
 |[[soapdenovo-trans-software|SOAPdenovo-Trans]]|1.03|''module load SOAPdenovo-Trans/1.03''| | |[[soapdenovo-trans-software|SOAPdenovo-Trans]]|1.03|''module load SOAPdenovo-Trans/1.03''| |
 |[[solexaqa-software|SolexaQA++]]|3.1.3|''module load SolexaQA++/3.1.3''| | |[[solexaqa-software|SolexaQA++]]|3.1.3|''module load SolexaQA++/3.1.3''| |
-|[[spades-software|spades]]|3.11.1|''module load spades/3.11.1''| |+|[[spades-software|spades]]|3.13.0|''module load spades/3.13.0''| |
 |[[sourmash-software|sourmash]]|1.0|''module load sourmash/1.0''| | |[[sourmash-software|sourmash]]|1.0|''module load sourmash/1.0''| |
 |[[speedseq-software|speedseq]]|0.1.2|''module load speedseq/0.1.2''| | |[[speedseq-software|speedseq]]|0.1.2|''module load speedseq/0.1.2''| |
 |splitstree|4.11.3|''module load splitstree/4.11.3''| | |splitstree|4.11.3|''module load splitstree/4.11.3''| |
 |spread|1.0.6|''module load spread/1.0.6''| | |spread|1.0.6|''module load spread/1.0.6''| |
-|[[sratoolkit-software|sratoolkit]]|2.8.2|''module load sratoolkit/2.8.2''| |+|[[squid-software|squid]]|1.9g|''module load squid/1.9g''| | 
 +|[[sratoolkit-software|sratoolkit]]|2.10.0|''module load sratoolkit/2.10.0''| |
 |[[sspace-software|sspace]]|3.0|''module load sspace/3.0''| | |[[sspace-software|sspace]]|3.0|''module load sspace/3.0''| |
 |[[sspace-longread-software|sspace-longread]]|1.1|''module load sspace-longread/1.1''| | |[[sspace-longread-software|sspace-longread]]|1.1|''module load sspace-longread/1.1''| |
 |[[stacks-software|stacks]]|1.24|''module load stacks/1.24''| | |[[stacks-software|stacks]]|1.24|''module load stacks/1.24''| |
 |staden|2.0.0b8|''module load staden/2.0.0b8''| | |staden|2.0.0b8|''module load staden/2.0.0b8''| |
-|[[star-software|star]]|2.5.3a|''module load star/2.5.3a''| |+|[[star-software|star]]|2.7.1a|''module load star/2.7.1a''| |
 |[[structure-software|structure]]|2.3.4|''module load structure/2.3.4'' | |[[structure-software|structure]]|2.3.4|''module load structure/2.3.4'' |
 |[[stringtie-software|stringtie]]|1.3.4d|''module load stringtie/1.3.4d''| | |[[stringtie-software|stringtie]]|1.3.4d|''module load stringtie/1.3.4d''| |
Line 267: Line 305:
 |[[trinotate-software|trinotate]]|2.0.2|''module load trinotate/2.0.2''| | |[[trinotate-software|trinotate]]|2.0.2|''module load trinotate/2.0.2''| |
 |[[twinscan-software|twinscan]]|3.5|''module load twinscan/3.5''| | |[[twinscan-software|twinscan]]|3.5|''module load twinscan/3.5''| |
-|[[umi-tools-software|umi-tools]]|  |''module load umi-tools/0.2.3''| | +|[[umi-tools-software|umi-tools]]| 0.2.3 |''module load umi-tools/0.2.3''| | 
-|[[usearch-software|usearch]]|  |''module load usearch/v7.0.1090''| |+|[[unicycler-software|unicycler]]| 0.4.7 |''module load unicycler/0.4.7''| | 
 +|[[usearch-software|usearch]]| v7.0.1090 |''module load usearch/v7.0.1090''| |
 |varscan|2.4.2|''module load varscan/2.4.2''| | |varscan|2.4.2|''module load varscan/2.4.2''| |
 |[[vcflib-software|vcflib]]|git-7f1575e|''module load vcflib/git-7f1575e''| | |[[vcflib-software|vcflib]]|git-7f1575e|''module load vcflib/git-7f1575e''| |
Line 274: Line 313:
 |[[velvet-software|velvet]]|1.2.10-kmer111|''module load velvet/1.2.10-kmer111''| | |[[velvet-software|velvet]]|1.2.10-kmer111|''module load velvet/1.2.10-kmer111''| |
 |[[vep-software|vep]]|92.1|''module load vep/92.1''| | |[[vep-software|vep]]|92.1|''module load vep/92.1''| |
-|[[vsearch-software|vsearch]]|2.8.0|''module load vsearch/2.8.0''| |+|[[viennarna-software|viennarna]]|2.4.14|''module load viennarna/2.4.14''| |
 |[[virusdetect-software|virusdetect]]|1.7|''module load virusdetect/1.7''| | |[[virusdetect-software|virusdetect]]|1.7|''module load virusdetect/1.7''| |
 |[[vntrseek-software|vntrseek]]|1.08|''module load vntrseek/1.08''| | |[[vntrseek-software|vntrseek]]|1.08|''module load vntrseek/1.08''| |
 +|[[vsearch-software|vsearch]]|2.8.0|''module load vsearch/2.8.0''| |
 |[[w2rap-software|w2rap]]|git-60781b6c|''module load w2rap/git-60781b6c''| | |[[w2rap-software|w2rap]]|git-60781b6c|''module load w2rap/git-60781b6c''| |
 |[[w2rap-contigger-software|w2rap-contigger]]|git-a43f5a05|''module load w2rap-contigger/git-a43f5a05''| | |[[w2rap-contigger-software|w2rap-contigger]]|git-a43f5a05|''module load w2rap-contigger/git-a43f5a05''| |
 |[[whatshap-software|whatshap]]|0.16|''module load whatshap/0.16''| | |[[whatshap-software|whatshap]]|0.16|''module load whatshap/0.16''| |
 |[[wise-software|wise]]|2.4.1|''module load wise/2.4.1''| | |[[wise-software|wise]]|2.4.1|''module load wise/2.4.1''| |
 +|[[wombat-software|wombat]]|2020-02-07|''module load wombat/2020-02-07''| |
 +|[[wtdbg2-software|wtdbg2]]|2.4|''module load wtdbg2/2.4''| |
  
 The source code for all environment modules can be found in [[https://github.com/ilri/hpc-environment-modules|ILRI's GitHub repository]]. The source code for all environment modules can be found in [[https://github.com/ilri/hpc-environment-modules|ILRI's GitHub repository]].
list-of-software.1548415786.txt.gz · Last modified: 2019/01/25 11:29 by aorth