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list-of-software [2019/01/25 14:29]
aorth
list-of-software [2019/04/10 23:38] (current)
aorth
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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''​| |
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 |[[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''​| |
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 |[[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''​| |
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 |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''​| |
 |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''​| |
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 |[[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''​| | |[[mash-software|mash]]|2.0|''​module load mash/​2.0''​| |
-|[[masurca-software|masurca]]|3.2.8|''​module load masurca/3.2.8''​| |+|[[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''​| |
 |maximus|0.2|''​module load maximus/​0.2''​| | |maximus|0.2|''​module load maximus/​0.2''​| |
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 |[[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]]|1.9|''​module load plink/​1.9''​| |
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 |[[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''​| |
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 |[[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''​| |
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 |[[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''​| |
list-of-software.1548415786.txt.gz · Last modified: 2019/01/25 14:29 by aorth