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list-of-software [2018/11/18 12:16]
aorth
list-of-software [2019/03/21 22:35] (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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 |[[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''​| | |[[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''​| |
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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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 |[[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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 |[[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]]|3.7.1|''​module load python/​3.7''​| |+|[[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''​| |
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 |[[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]]|3.5.2|''​module load R/​3.5''​| |
 |[[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''​| |
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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.1542532578.txt.gz · Last modified: 2018/11/18 12:16 by aorth