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list-of-software [2018/09/16 10:45]
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list-of-software [2019/08/08 23:11] (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]]|2.0.2|''​module load abyss/2.0.2''​| |+|[[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 25: Line 26:
 |bayescan|2.1|''​module load bayescan/​2.1''​| | |bayescan|2.1|''​module load bayescan/​2.1''​| |
 |[[bcftools-software|bcftools]]|1.8|''​module load bcftools/​1.8''​| | |[[bcftools-software|bcftools]]|1.8|''​module load bcftools/​1.8''​| |
-|[[beagle-software|beagle]]|2.1.2|''​module load beagle/2.1.2''​| | +|[[beagle-software|beagle]]|3.0.2|''​module load beagle/3.0.2''​| | 
-|[[beast-software|beast]]|1.8.3|''​module load beast/1.8.3''​| |+|[[beast-software|beast]]|1.10.2|''​module load beast/1.10.2''​| |
 |[[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]]|2.25.0|''​module load bedtools/​2.25.0''​| |
Line 43: Line 44:
 |[[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''​| |
-|[[canu-software|canu]]|1.6|''​module load canu/1.6''​| |+|[[canu-software|canu]]|1.8|''​module load canu/1.8''​| |
 |cap3|latest|''​module load cap3/​latest''​| | |cap3|latest|''​module load cap3/​latest''​| |
-|[[cd-hit-software|cd-hit]]|4.6.6|''​module load cd-hit/4.6.6''​| |+|[[cd-hit-software|cd-hit]]|4.6.8|''​module load cd-hit/4.6.8''​| |
 |[[cegma-software|cegma]]|v2.5|''​module load cegma/​v2.5''​| | |[[cegma-software|cegma]]|v2.5|''​module load cegma/​v2.5''​| |
 |celera-wgs|6.1|''​module load celera-wgs/​6.1''​| | |celera-wgs|6.1|''​module load celera-wgs/​6.1''​| |
Line 60: Line 61:
 |[[corset-software|corset]]|1.06|''​module load corset/​1.06''​| | |[[corset-software|corset]]|1.06|''​module load corset/​1.06''​| |
 |cufflinks|2.2.1|''​module load cufflinks/​2.2.1''​| | |cufflinks|2.2.1|''​module load cufflinks/​2.2.1''​| |
-|[[cutadapt-software|cutadapt]]|v1.8.1|''​module load cutadapt/v1.8.1''​| |+|[[cutadapt-software|cutadapt]]|1.18|''​module load cutadapt/1.18''​| | 
 +|[[dextractor-software|dextractor]]|git-a7f50c52|''​module load dextractor/​git-a7f50c52''​| |
 |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''​| |
-|[[ea-utils-software|ea-utils]]|1.1.2|''​module load ea-utils/1.1.2''​| |+|[[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''​ | |
 |eigenstrat|3.0|''​module load eigenstrat/​3.0''​| | |eigenstrat|3.0|''​module load eigenstrat/​3.0''​| |
Line 72: Line 74:
 |[[express-software|express]]|1.5.1|''​module load express/​1.5.1''​| | |[[express-software|express]]|1.5.1|''​module load express/​1.5.1''​| |
 |[[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]]|0.11.5|''​module load fastqc/​0.11.5''​| |+|[[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''​| |
 |[[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''​| |
Line 81: Line 83:
 |[[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 ]]|1.19|''​module load fraggenescan/​1.19''​| |
 |[[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''​| |
-|[[gatk-software|GATK ]]|3.7.0|''​module load gatk/3.7.0''​| |+|[[gatk-software|GATK ]]|4.0.10.1|''​module load gatk/4.0.10.1''​| |
 |[[gapfiller-software|gapfiller]]|1.10|''​module load gapfiller/​1.10''​| | |[[gapfiller-software|gapfiller]]|1.10|''​module load gapfiller/​1.10''​| |
 |[[geneid-software|geneid]]|1.4.4|''​module load geneid/​1.4.4''​| | |[[geneid-software|geneid]]|1.4.4|''​module load geneid/​1.4.4''​| |
Line 93: Line 96:
 |glu|1.0b3-prerelease4|''​module load glu/​1.0b3-prerelease4''​| | |glu|1.0b3-prerelease4|''​module load glu/​1.0b3-prerelease4''​| |
 |[[gmap-software|gmap]]|2015-12-31|''​module load gmap/​2015-12-31''​| | |[[gmap-software|gmap]]|2015-12-31|''​module load gmap/​2015-12-31''​| |
 +|[[graphmap-software|graphmap]]|0.5.2|''​module load graphmap/​0.5.2''​| |
 |[[grom-rd-software|grom-rd]]|1.0|''​module load grom-rd/​1.0''​| | |[[grom-rd-software|grom-rd]]|1.0|''​module load grom-rd/​1.0''​| |
 |[[gromacs-software|gromacs]]|2018.2|''​module load gromacs/​2018.2''​| | |[[gromacs-software|gromacs]]|2018.2|''​module load gromacs/​2018.2''​| |
Line 103: Line 107:
 |[[hmmer-software|hmmer]]|3.1b2|''​module load hmmer/​3.1b2''​| | |[[hmmer-software|hmmer]]|3.1b2|''​module load hmmer/​3.1b2''​| |
 |[[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]]|2.0.5|''​module load hisat2/2.0.5''​| | +|[[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]]|1.8|''​module load htslib/​1.8''​| |
 |[[igblast-software|igblast]]|1.6.0|''​module load igblast/​1.6.0''​| | |[[igblast-software|igblast]]|1.6.0|''​module load igblast/​1.6.0''​| |
Line 110: Line 114:
 |[[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''​| |
-|[[java-software|java]]|1.8|''​module load java/​1.8''​| | 
 |[[jellyfish-software|jellyfish]]|2.2.9|''​module load jellyfish/​2.2.9''​| | |[[jellyfish-software|jellyfish]]|2.2.9|''​module load jellyfish/​2.2.9''​| |
 |jMHC|1.5.0929|''​module load jMHC/​1.5.0929''​| | |jMHC|1.5.0929|''​module load jMHC/​1.5.0929''​| |
Line 118: Line 122:
 |[[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''​| |
 |[[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 127: Line 133:
 |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''​| |
 |[[mash-software|mash]]|2.0|''​module load mash/​2.0''​| | |[[mash-software|mash]]|2.0|''​module load mash/​2.0''​| |
 +|[[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''​| |
-|[[masurca-software|masurca]]|2.3.2|''​module load masurca/​2.3.2''​| | 
 |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''​| |
-|[[megahit-software|megahit]]|git-02102e1b|''​module load megahit/git-02102e1b''​| |+|[[mecat-software|MECAT]]|git-d04bfa84|''​module load MECAT/git-d04bfa84''​| | 
 +|[[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''​| |
 |[[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''​| |
 |[[migmap-software|migmap]]|1.0.2|''​module load migmap/​1.0.2''​| | |[[migmap-software|migmap]]|1.0.2|''​module load migmap/​1.0.2''​| |
 +|[[miniasm-software|miniasm]]|0.3|''​module load miniasm/​0.3''​| |
 +|[[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''​| |
Line 154: Line 167:
 |[[muscle-software|muscle]]|3.8.31|''​module load muscle/​3.8.31''​| ​ | |[[muscle-software|muscle]]|3.8.31|''​module load muscle/​3.8.31''​| ​ |
 |[[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''​| |
 |[[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''​| |
Line 167: Line 181:
 |[[paml-software|paml]]|4.9a|''​module load paml/​4.9a''​| | |[[paml-software|paml]]|4.9a|''​module load paml/​4.9a''​| |
 |[[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''​| ​ |
 |[[pear-software|pear]]|git-2c309dc|''​module load pear/​git-2c309dc''​| | |[[pear-software|pear]]|git-2c309dc|''​module load pear/​git-2c309dc''​| |
 +|[[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]]|5.22.3|''​module load perl/​5.22.3''​| |
Line 177: Line 193:
 |[[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]]|1.23|''​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]]|1.9|''​module load plink/​1.9''​| |
Line 185: Line 202:
 |[[prokka-software|prokka]]|1.11|''​module load prokka/​1.11''​| | |[[prokka-software|prokka]]|1.11|''​module load prokka/​1.11''​| |
 |[[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]]|3.6.2|''​module load python/3.6.2''​| |+|[[python-software|python]]|3.7.2|''​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''​| |
Line 191: Line 208:
 |[[quast-software|quast]]|4.5|''​module load quast/​4.5''​| | |[[quast-software|quast]]|4.5|''​module load quast/​4.5''​| |
 |[[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]]|3.5.1|''​module load R/3.5.1''​| |+|[[r-software|R]]|3.6.1|''​module load R/3.6''​| | 
 +|[[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''​| |
-|rstudio|v0.97.551|''​module load rstudio/​v0.97.551''​| | 
 |rapsearch|2.10|''​module load rapsearch/​2.10''​| | |rapsearch|2.10|''​module load rapsearch/​2.10''​| |
 |[[ratt-software|RATT]]|r18|''​module load ratt/​r18''​| | |[[ratt-software|RATT]]|r18|''​module load ratt/​r18''​| |
Line 202: Line 219:
 |[[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''​| |
-|[[rsem-software|RSEM]]|1.2.21|''​module load RSEM/1.2.21''​| |+|[[rsem-software|RSEM]]|1.3.1|''​module load RSEM/1.3.1''​| |
 |[[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''​| |
Line 210: Line 227:
 |[[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''​| |
 +|[[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]]|0.7.2|''​module load seqkit/​0.7.2''​| |
Line 219: Line 237:
 |[[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''​| |
 |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 229: Line 248:
 |[[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''​| |
Line 239: Line 258:
 |[[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 257: Line 276:
 |[[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 271: Line 291:
 |[[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''​| |
 +|[[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.1537083943.txt.gz · Last modified: 2018/09/16 10:45 by aorth