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list-of-software [2019/02/15 02:29]
aorth
list-of-software [2019/10/08 12:15]
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 ​  ^
Line 24: Line 24:
 |[[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''​| |
Line 83: Line 85:
 |[[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''​| |
Line 107: Line 110:
 |[[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''​| | |[[igblast-software|igblast]]|1.6.0|''​module load igblast/​1.6.0''​| |
 |[[igrec-software|igrec]]|3.0.0|''​module load igrec/​3.0.0''​| | |[[igrec-software|igrec]]|3.0.0|''​module load igrec/​3.0.0''​| |
 |[[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 125: Line 129:
 |[[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 132: Line 136:
 |[[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''​| | |[[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''​| |
 +|[[marginpolish-software|marginpolish]]|1.0.0|''​module load marginpolish/​1.0.0''​| |
 |[[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''​| |
 |[[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''​| |
 |[[metis-software|metis]]|5.1.0|''​module load metis/​5.1.0''​| | |[[metis-software|metis]]|5.1.0|''​module load metis/​5.1.0''​| |
Line 179: Line 187:
 |[[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]]|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 188: Line 197:
 |[[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''​| |
Line 200: Line 209:
 |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]]|2019.7|''​module load qiime2/2019.7''​| |
 |[[quast-software|quast]]|4.5|''​module load quast/​4.5''​| | |[[quast-software|quast]]|4.5|''​module load quast/​4.5''​| |
 +|[[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''​| |
Line 217: Line 227:
 |[[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''​| |
Line 228: Line 238:
 |[[seqtk-software|seqtk]]|1.2-r102|''​module load seqtk/​1.2-r102''​| | |[[seqtk-software|seqtk]]|1.2-r102|''​module load seqtk/​1.2-r102''​| |
 |[[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]]|0.2.0|''​module load shasta/​0.2.0''​| |
 |[[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 242: Line 255:
 |[[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 252: Line 265:
 |[[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 270: Line 283:
 |[[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 284: Line 298:
 |[[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.txt · Last modified: 2019/11/04 10:43 by aorth