Difference between revisions of "Biocluster Applications"

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|-
 
|-
 
|454
 
|454
−
|2.8
+
|2.6, 2.7, 2.8
 
|-
 
|-
 
|AbundantOTU+
 
|AbundantOTU+
Line 11: Line 11:
 
|-
 
|-
 
|abyss
 
|abyss
−
|1.3.4
+
|1.2.5, 1.3.3, 1.3.4
 
|-
 
|-
 
|afni
 
|afni
Line 53: Line 53:
 
|-
 
|-
 
|bedtools
 
|bedtools
−
|2.17.0
+
|2.10.0, 2.10.1, 2.17.0
 
|-
 
|-
 
|biodatabase
 
|biodatabase
Line 62: Line 62:
 
|-
 
|-
 
|blast+
 
|blast+
−
|2.2.28+
+
|2.2.25+, 2.2.28+
 
|-
 
|-
 
|blast-intel
 
|blast-intel
Line 68: Line 68:
 
|-
 
|-
 
|blast
 
|blast
−
|2.2.26
+
|2.2.25, 2.2.26
 
|-
 
|-
 
|blast2go
 
|blast2go
Line 83: Line 83:
 
|-
 
|-
 
|bowtie
 
|bowtie
−
|1.0.0
+
|0.12.8, 0.12.9, 1.0.0
 
|-
 
|-
 
|bowtie2
 
|bowtie2
−
|2.1.0
+
|2.0.0-beta6, 2.0.2, 2.0.5, 2.1.0
 
|-
 
|-
 
|breseq
 
|breseq
Line 92: Line 92:
 
|-
 
|-
 
|bwa
 
|bwa
−
|0.7.5a
+
|0.5.9, 0.7.5a
 
|-
 
|-
 
|cafe
 
|cafe
−
|3.0
+
|2.2, 3.0
 
|-
 
|-
 
|casava
 
|casava
Line 101: Line 101:
 
|-
 
|-
 
|cd-hit
 
|cd-hit
−
|4.6.1
+
|4.6, 4.6.1
 
|-
 
|-
 
|cdbfasta
 
|cdbfasta
Line 113: Line 113:
 
|-
 
|-
 
|chimera
 
|chimera
−
|1.6.2
+
|1.5.3, 1.6.2
 
|-
 
|-
 
|cisgenome
 
|cisgenome
Line 128: Line 128:
 
|-
 
|-
 
|cufflinks
 
|cufflinks
−
|2.1.1
+
|1.1.0, 1.3.0, 2.0.2, 2.1.1
 
|-
 
|-
 
|cutadapt
 
|cutadapt
Line 134: Line 134:
 
|-
 
|-
 
|cytoscape
 
|cytoscape
−
|2.8.3
+
|2.8.1, 2.8.3
 
|-
 
|-
 
|EagleView
 
|EagleView
Line 140: Line 140:
 
|-
 
|-
 
|efiest
 
|efiest
−
|devel
+
|alpha, devel
 
|-
 
|-
 
|EMBOSS
 
|EMBOSS
Line 176: Line 176:
 
|-
 
|-
 
|gatk
 
|gatk
−
|2.6-4
+
|1.6-5, 1.6-13, 2.5-2, 2.6-4
 
|-
 
|-
 
|gcc
 
|gcc
Line 197: Line 197:
 
|-
 
|-
 
|gmap
 
|gmap
−
|2013-03-31
+
|2011-09-14, 2013-03-31
 
|-
 
|-
 
|gmes
 
|gmes
Line 215: Line 215:
 
|-
 
|-
 
|hmmer
 
|hmmer
−
|3.0
+
|2.3.2, 3.0
 
|-
 
|-
 
|htseq
 
|htseq
Line 239: Line 239:
 
|-
 
|-
 
|infernal
 
|infernal
−
|1.1rc2
+
|1.1rc1, 1.1rc2
 
|-
 
|-
 
|inparanoid
 
|inparanoid
Line 245: Line 245:
 
|-
 
|-
 
|iprscan
 
|iprscan
−
|5.45
+
|4.8, 5.44, 5.45
 
|-
 
|-
 
|java
 
|java
−
|1.7.0_07
+
|1.6.0_41, 1.7.0_06-i386, 1.7.0_07
 
|-
 
|-
 
|jellyfish
 
|jellyfish
−
|1.1.11
+
|1.1.6, 1.1.11
 
|-
 
|-
 
|khmer
 
|khmer
Line 278: Line 278:
 
|-
 
|-
 
|lua
 
|lua
−
|5.2.2
+
|5.1.4, 5.2.2
 
|-
 
|-
 
|MACS
 
|MACS
−
|2.0.10
+
|1.4.2, 2.0.10
 
|-
 
|-
 
|mafft
 
|mafft
Line 296: Line 296:
 
|-
 
|-
 
|MEGAN
 
|MEGAN
−
|5.1.0
+
|4.70.4, 5.1.0
 
|-
 
|-
 
|meme
 
|meme
Line 308: Line 308:
 
|-
 
|-
 
|MetaVelvet
 
|MetaVelvet
−
|1.2.02-kmer245
+
|1.2.02, 1.2.02-kmer245
 
|-
 
|-
 
|mfinder
 
|mfinder
Line 320: Line 320:
 
|-
 
|-
 
|ModalClust
 
|ModalClust
−
|0.3
+
|0.2, 0.3
 
|-
 
|-
 
|mothur
 
|mothur
−
|1.32.1
+
|1.8, 1.28.0, 1.31.2, 1.32.0, 1.32.1
 
|-
 
|-
 
|mpich
 
|mpich
Line 329: Line 329:
 
|-
 
|-
 
|mpich2
 
|mpich2
−
|1.5
+
|1.4.1p1, 1.5
 
|-
 
|-
 
|msort
 
|msort
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|-
 
|-
 
|novocraft
 
|novocraft
−
|3.02
+
|2.08, 2.08.02, 2.08.03, 3.00.01, 3.00.02, 3.00.05, 3.02
 
|-
 
|-
 
|oasas-kmer245
 
|oasas-kmer245
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|-
 
|-
 
|openmpi
 
|openmpi
−
|1.6.3
+
|1.4.3, 1.6.3
 
|-
 
|-
 
|orthomcl
 
|orthomcl
−
|2.0.7
+
|2.0.2, 2.0.7
 
|-
 
|-
 
|paml
 
|paml
Line 395: Line 395:
 
|-
 
|-
 
|picard-tools
 
|picard-tools
−
|1.90
+
|1.34, 1.73, 1.90
 
|-
 
|-
 
|polyphen
 
|polyphen
Line 401: Line 401:
 
|-
 
|-
 
|pplacer
 
|pplacer
−
|1.1
+
|1.0, 1.1
 
|-
 
|-
 
|prank
 
|prank
Line 407: Line 407:
 
|-
 
|-
 
|prodigal
 
|prodigal
−
|2.2
+
|2.0, 2.2
 
|-
 
|-
 
|python
 
|python
−
|3.2.3
+
|2.6.6, 2.7.3(default), 2.7.3-sqlite, 2.7.5-galaxy, 3.2.3
 
|-
 
|-
 
|qiime
 
|qiime
−
|1.7.0
+
|1.3.0, 1.5.0, 1.6.0, 1.7.0
 
|-
 
|-
 
|quake
 
|quake
Line 422: Line 422:
 
|-
 
|-
 
|quest
 
|quest
−
|devel
+
|alpha, devel
 
|-
 
|-
 
|R
 
|R
−
|3.0.2
+
|2.15.0, 2.15.1, 2.15.2, 3.0.0(default), 3.0.2
 
|-
 
|-
 
|RAxML
 
|RAxML
Line 431: Line 431:
 
|-
 
|-
 
|ray
 
|ray
−
|2.30
+
|2.20, 2.30
 
|-
 
|-
 
|rdp_classifier
 
|rdp_classifier
Line 455: Line 455:
 
|-
 
|-
 
|samtools
 
|samtools
−
|0.1.16
+
|0.1.16, 0.1.18, 0.1.19
−
|-
 
−
|samtools
 
−
|0.1.18
 
−
|-
 
−
|samtools
 
−
|0.1.19
 
 
|-
 
|-
 
|sam_comp
 
|sam_comp
Line 473: Line 467:
 
|-
 
|-
 
|smrtanalysis
 
|smrtanalysis
−
|1.4.0
+
|1.4.0, 2.0.1
−
|-
 
−
|smrtanalysis
 
−
|2.0.1
 
 
|-
 
|-
 
|SnpEff
 
|SnpEff
−
|3.2
+
|3.2, 3.3e
−
|-
 
−
|SnpEff
 
−
|3.3e
 
 
|-
 
|-
 
|SOAP2
 
|SOAP2
Line 497: Line 485:
 
|-
 
|-
 
|SOAPec
 
|SOAPec
−
|2.01
+
|2.01, 2.02
−
|-
 
−
|SOAPec
 
−
|2.02
 
 
|-
 
|-
 
|SOAPErrorCorrection
 
|SOAPErrorCorrection
Line 512: Line 497:
 
|-
 
|-
 
|speciateit
 
|speciateit
−
|184(default)
+
|184(default), template
−
|-
 
−
|speciateit
 
−
|template
 
 
|-
 
|-
 
|speciatetest
 
|speciatetest
Line 533: Line 515:
 
|-
 
|-
 
|stacks
 
|stacks
−
|0.9996
+
|0.9996, 0.99994
−
|-
 
−
|stacks
 
−
|0.99994
 
 
|-
 
|-
 
|structure
 
|structure
Line 560: Line 539:
 
|-
 
|-
 
|tophat2
 
|tophat2
−
|2.0.4
+
|2.0.4, 2.0.5, 2.0.6, 2.0.7, 2.0.8, 2.0.10(default)
−
|-
 
−
|tophat2
 
−
|2.0.5
 
−
|-
 
−
|tophat2
 
−
|2.0.6
 
−
|-
 
−
|tophat2
 
−
|2.0.7
 
−
|-
 
−
|tophat2
 
−
|2.0.8
 
−
|-
 
−
|tophat2
 
−
|2.0.10(default)
 
 
|-
 
|-
 
|treemix
 
|treemix
Line 584: Line 548:
 
|-
 
|-
 
|trimmomatic
 
|trimmomatic
−
|0.22
+
|0.22, 0.27, 0.30
−
|-
 
−
|trimmomatic
 
−
|0.27
 
−
|-
 
−
|trimmomatic
 
−
|0.30
 
 
|-
 
|-
 
|trinityrnaseq-intel
 
|trinityrnaseq-intel
Line 596: Line 554:
 
|-
 
|-
 
|trinityrnaseq
 
|trinityrnaseq
−
|r2012-06-08
+
|r2012-06-08, r2013-02-25, r2013-08-14
−
|-
 
−
|trinityrnaseq
 
−
|r2013-02-25
 
−
|-
 
−
|trinityrnaseq
 
−
|r2013-08-14
 
 
|-
 
|-
 
|trinotate
 
|trinotate
Line 614: Line 566:
 
|-
 
|-
 
|usearch
 
|usearch
−
|6.0.307
+
|6.0.307, 6.1.544, 7.0.959
−
|-
 
−
|usearch
 
−
|6.1.544
 
−
|-
 
−
|usearch
 
−
|7.0.959
 
 
|-
 
|-
 
|USeq
 
|USeq
Line 626: Line 572:
 
|-
 
|-
 
|vcftools
 
|vcftools
−
|0.1.7
+
|0.1.7, 0.1.11
−
|-
 
−
|vcftools
 
−
|0.1.11
 
 
|-
 
|-
 
|velvet-kmer245
 
|velvet-kmer245
Line 635: Line 578:
 
|-
 
|-
 
|velvet
 
|velvet
−
|1.1.04
+
|1.1.04, 1.2.08, 1.2.10
−
|-
 
−
|velvet
 
−
|1.2.08
 
−
|-
 
−
|velvet
 
−
|1.2.10
 
 
|-
 
|-
 
|velvetOptimiser
 
|velvetOptimiser

Revision as of 00:46, 16 February 2014

Application Installed Version
454 2.6, 2.7, 2.8
AbundantOTU+ 0.91b
abyss 1.2.5, 1.3.3, 1.3.4
afni 2011_12_21_2014
allpathslg 42911
amos 3.1.0
AmpliconNoise 1.2.7
art 20110922
artemis 14.0
augustus 2.6.1
b2g4pipe 2.5
babraham bioinformatics
bali-phy 2.1.1
bam2fastq 1.1.0
bamtools 0.9.0
bcbio-nextgen 0.6.5
bedtools 2.10.0, 2.10.1, 2.17.0
biodatabase 1.0
biopieces 0.48
blast+ 2.2.25+, 2.2.28+
blast-intel 2.2.26
blast 2.2.25, 2.2.26
blast2go 2.5
blat 0.34
boost-intel 1.54
boost 1.54
bowtie 0.12.8, 0.12.9, 1.0.0
bowtie2 2.0.0-beta6, 2.0.2, 2.0.5, 2.1.0
breseq 0.24
bwa 0.5.9, 0.7.5a
cafe 2.2, 3.0
casava 1.8.2
cd-hit 4.6, 4.6.1
cdbfasta 0.99
cegma v2.4.010312
chance 1.0
chimera 1.5.3, 1.6.2
cisgenome 2.0
ClonalFrame 1.2
clustalo 1.2.0
clustalw 2.1
cufflinks 1.1.0, 1.3.0, 2.0.2, 2.1.1
cutadapt 1.2
cytoscape 2.8.1, 2.8.3
EagleView 2.2
efiest alpha, devel
EMBOSS 6.5.7
erange 3.2.1
estscan 3.0.3
fasta 36.3.5d
fasta_splitter 1
fastqc 0.10.1
fastsimcoal2 1.1.1
fasttree 2.1.7
fastx_toolkit 0.0.13
findpeaks 3.1.9.2
freebayes 0.9.6
gatk 1.6-5, 1.6-13, 2.5-2, 2.6-4
gcc 4.8.1
geneid 1.0
genomer 0.0.10
genometools 1.5.1
gff 2.1
glimmer 3.02
gmap 2011-09-14, 2013-03-31
gmes v2.3e
gnuplot 4.6.3
graphviz 2.32.0
gsl 1.16
hmmer-mpi 2.32-MPI-0.92
hmmer 2.3.2, 3.0
htseq 0.5.4
icc 2013.5.192
idba-ud 1.1.0
IGV 2.1.24
IGVTools 2.1.24
IMAGE 2.33
ImageMagick 6.7.8-9
infernal 1.1rc1, 1.1rc2
inparanoid 4.1
iprscan 4.8, 5.44, 5.45
java 1.6.0_41, 1.7.0_06-i386, 1.7.0_07
jellyfish 1.1.6, 1.1.11
khmer 2013-05-06
kmergenie 1.5854
krona 2.2
lamarc 2.1.8
last 278
lastz 1.02.00
libstree 0.4.2
LR-TRIRLS 20060531
lua 5.1.4, 5.2.2
MACS 1.4.2, 2.0.10
mafft 6.953
matlab-runtime r2012b
matlab 7.11.0.584
mcl 12-068
MEGAN 4.70.4, 5.1.0
meme 4.9.0
MetaGeneMark 2010
metAMOS 1.2
MetaVelvet 1.2.02, 1.2.02-kmer245
mfinder 1.2
mira 3.2.1
MOCAT 1.1
ModalClust 0.2, 0.3
mothur 1.8, 1.28.0, 1.31.2, 1.32.0, 1.32.1
mpich 3.0.4
mpich2 1.4.1p1, 1.5
msort 1.0
MUMmer 3.23
muscle 3.8.31
novocraft 2.08, 2.08.02, 2.08.03, 3.00.01, 3.00.02, 3.00.05, 3.02
oasas-kmer245 0.2.8
oasas 0.2.8
OLB 1.9.4
openmpi-intel 1.6.3
openmpi 1.4.3, 1.6.3
orthomcl 2.0.2, 2.0.7
paml 4.4
parallel 20121122
pathway-tools 16.5
PBJelly 12.9.14
peaksplitter 1.0
perfsuite 1.0.0
perl 5.16.1
pfamscan 1.0
phred 0.020425.c
phylip 3.69
phymmbl 4.0
picard-tools 1.34, 1.73, 1.90
polyphen 2.2.2
pplacer 1.0, 1.1
prank 121002
prodigal 2.0, 2.2
python 2.6.6, 2.7.3(default), 2.7.3-sqlite, 2.7.5-galaxy, 3.2.3
qiime 1.3.0, 1.5.0, 1.6.0, 1.7.0
quake 0.3.4
quast 2.2
quest alpha, devel
R 2.15.0, 2.15.1, 2.15.2, 3.0.0(default), 3.0.2
RAxML 7.3.0
ray 2.20, 2.30
rdp_classifier 2.5
rdxplorer 3.2
repeatmasker 3.28
rockhopper 1.2
rsa-tools 2012-10-09
rstudio 0.97.312
ruby 1.9.3
samtools 0.1.16, 0.1.18, 0.1.19
sam_comp 0.7
SICER 1.1
signalp 4.1
smrtanalysis 1.4.0, 2.0.1
SnpEff 3.2, 3.3e
SOAP2 2.2
SOAPdenovo-Trans 1.02
SOAPdenovo 2.04
SOAPdenovo2 r240
SOAPec 2.01, 2.02
SOAPErrorCorrection 0.04
SOAPGapCloser 1.12
SOAPprepare 0.1
speciateit 184(default), template
speciatetest 184
speciate_it 184(default)
sratoolkit 2.1.16
srna-tools 20130118
ssaha2 2.5.5
stacks 0.9996, 0.99994
structure 2.3.4
subread 3.1.6
supfam 1.75
tabix 0.2.6
tcoffee 10-r1613
tmhmm 2.0
tophat 1.4.1
tophat2 2.0.4, 2.0.5, 2.0.6, 2.0.7, 2.0.8, 2.0.10(default)
treemix 1.12
trf 4.04
trimmomatic 0.22, 0.27, 0.30
trinityrnaseq-intel r2013-02-25
trinityrnaseq r2012-06-08, r2013-02-25, r2013-08-14
trinotate trinotate_r20130826
truesight 0.06
uchime 4.2.40
usearch 6.0.307, 6.1.544, 7.0.959
USeq 8.5.1
vcftools 0.1.7, 0.1.11
velvet-kmer245 1.2.10
velvet 1.1.04, 1.2.08, 1.2.10
velvetOptimiser 2.2.5
wessim 1.0
wgs 7.0
wise 2.2.3-rc7
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