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list-of-software [2018/06/12 18:07]
aorth
list-of-software [2018/10/15 16:27] (current)
aorth
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 |[[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 85: Line 85:
 |[[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 94: Line 94:
 |[[gmap-software|gmap]]|2015-12-31|''​module load gmap/​2015-12-31''​| | |[[gmap-software|gmap]]|2015-12-31|''​module load gmap/​2015-12-31''​| |
 |[[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''​| |
 |[[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''​| |
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 |[[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]]|0.6.1|''​module load htseq/​0.6.1''​| |
 |[[htslib-software|htslib]]|1.8|''​module load htslib/​1.8''​| | |[[htslib-software|htslib]]|1.8|''​module load htslib/​1.8''​| |
Line 133: Line 134:
 |[[masurca-software|masurca]]|2.3.2|''​module load masurca/​2.3.2''​| | |[[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''​| |
 |[[megahit-software|megahit]]|git-02102e1b|''​module load megahit/​git-02102e1b''​| | |[[megahit-software|megahit]]|git-02102e1b|''​module load megahit/​git-02102e1b''​| |
 |megan|4.70.4|''​module load megan/​4.70.4''​| | |megan|4.70.4|''​module load megan/​4.70.4''​| |
Line 172: Line 174:
 |phred|0.990722.f|''​module load phred/​0.990722.f''​| | |phred|0.990722.f|''​module load phred/​0.990722.f''​| |
 |[[phylip-software|phylip]]|3.696|''​module load phylip/​3.696''​| | |[[phylip-software|phylip]]|3.696|''​module load phylip/​3.696''​| |
-|[[phyml-software|phyml]]|20120412|''​module load phyml/20120412''​| |+|[[phyml-software|phyml]]|3.3.20180621|''​module load phyml/3.3.20180621''​| |
 |[[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''​| |
Line 186: Line 188:
 |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]]|2018.4|''​module load qiime2/​2018.4''​| |+|[[qiime2-software|qiime2]]|2018.6|''​module load qiime2/​2018.6''​| |
 |[[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]]|3.4.4|''​module load R/3.4.4''​| |+|[[r-software|R]]|3.5.1|''​module load R/3.5.1''​| |
 |[[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''​| | |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''​| |
-|[[raxml-software|RAxML]]|8.2.0|''​module load RAxML/8.2.0''​| |+|[[raxml-software|RAxML]]|8.2.12|''​module load RAxML/8.2.12''​| |
 |[[ray-software|ray]]|2.3.1|''​module load ray/​2.3.1''​| | |[[ray-software|ray]]|2.3.1|''​module load ray/​2.3.1''​| |
 |[[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''​| |
Line 237: Line 239:
 |[[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]]|2.5.2b|''​module load star/2.5.2b''​| |+|[[star-software|star]]|2.5.3a|''​module load star/2.5.3a''​| |
 |[[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''​| |
 +|[[subread-software|subread]]|1.6.2|''​module load subread/​1.6.2''​| |
 |svmlight|V6.02|''​module load svmlight/​V6.02''​| | |svmlight|V6.02|''​module load svmlight/​V6.02''​| |
 |tabix|git-76b4bbdf|''​module load tabix/​git-76b4bbdf''​| | |tabix|git-76b4bbdf|''​module load tabix/​git-76b4bbdf''​| |
Line 266: Line 269:
 |[[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''​| |
 |[[wise-software|wise]]|2.4.1|''​module load wise/​2.4.1''​| | |[[wise-software|wise]]|2.4.1|''​module load wise/​2.4.1''​| |
  
 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.1528816030.txt.gz · Last modified: 2018/06/12 18:07 by aorth