Difference between revisions of "Biocluster Applications"

From Carl R. Woese Institute for Genomic Biology - University of Illinois Urbana-Champaign
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!Application
 
!Application
−
!Version
+
!Installed Version
 
|-
 
|-
 
|454
 
|454
−
|2.6, 2.7, 2.8
+
|2.6, 2.7
 +
|-
 +
|454
 +
|2.8
 
|-
 
|-
 
|AbundantOTU+
 
|AbundantOTU+
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|-
 
|-
 
|abyss
 
|abyss
−
|1.2.5, 1.3.3, 1.3.4
+
|1.2.5, 1.3.3
 +
|-
 +
|abyss
 +
|1.3.4
 
|-
 
|-
 
|afni
 
|afni
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|-
 
|bedtools
 
|bedtools
−
|2.10.0, 2.10.1, 2.17.0
+
|2.10.0, 2.10.1
 +
|-
 +
|bedtools
 +
|2.17.0
 
|-
 
|-
 
|biodatabase
 
|biodatabase
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|-
 
|bowtie
 
|bowtie
−
|0.12.8, 0.12.9, 1.0.0
+
|0.12.8, 0.12.9
 +
|-
 +
|bowtie
 +
|1.0.0
 +
|-
 +
|bowtie2
 +
|2.0.0-beta6, 2.0.2, 2.1.0
 
|-
 
|-
 
|bowtie2
 
|bowtie2
−
|2.0.0-beta6, 2.0.2, 2.0.5, 2.1.0
+
|2.0.5
 
|-
 
|-
 
|breseq
 
|breseq
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|-
 
|cafe
 
|cafe
−
|2.2, 3.0
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|2.2
 +
|-
 +
|cafe
 +
|3.0
 
|-
 
|-
 
|casava
 
|casava
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|-
 
|cufflinks
 
|cufflinks
−
|1.1.0, 1.3.0, 2.0.2, 2.1.1
+
|1.1.0, 1.3.0, 2.1.1
 +
|-
 +
|cufflinks
 +
|2.0.2
 
|-
 
|-
 
|cutadapt
 
|cutadapt
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|-
 
|gatk
 
|gatk
−
|1.6-5, 1.6-13, 2.5-2, 2.6-4
+
|1.6-5, 1.6-13, 2.6-4
 +
|-
 +
|gatk
 +
|2.5-2
 
|-
 
|-
 
|gcc
 
|gcc
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|-
 
|iprscan
 
|iprscan
−
|4.8, 5.44, 5.45
+
|4.8, 5.44
 +
|-
 +
|iprscan
 +
|5.45
 +
|-
 +
|java
 +
|1.6.0_41, 1.7.0_06-i386
 
|-
 
|-
 
|java
 
|java
−
|1.6.0_41, 1.7.0_06-i386, 1.7.0_07
+
|1.7.0_07
 
|-
 
|-
 
|jellyfish
 
|jellyfish
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|-
 
|MACS
 
|MACS
−
|1.4.2, 2.0.10
+
|1.4.2
 +
|-
 +
|MACS
 +
|2.0.10
 
|-
 
|-
 
|mafft
 
|mafft
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|-
 
|mothur
 
|mothur
−
|1.8, 1.28.0, 1.31.2, 1.32.0, 1.32.1
+
|1.8
 +
|-
 +
|mothur
 +
|1.28.0, 1.31.2, 1.32.1
 +
|-
 +
|mothur
 +
|1.32.0
 
|-
 
|-
 
|mpich
 
|mpich
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|-
 
|novocraft
 
|novocraft
−
|2.08, 2.08.02, 2.08.03, 3.00.01, 3.00.02, 3.00.05, 3.02
+
|2.08, 2.08.02, 3.00.01, 3.00.05
 +
|-
 +
|novocraft
 +
|2.08.03
 +
|-
 +
|novocraft
 +
|3.00.02
 +
|-
 +
|novocraft
 +
|3.02
 
|-
 
|-
 
|oasas-kmer245
 
|oasas-kmer245
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|-
 
|-
 
|orthomcl
 
|orthomcl
−
|2.0.2, 2.0.7
+
|2.0.2
 +
|-
 +
|orthomcl
 +
|2.0.7
 
|-
 
|-
 
|paml
 
|paml
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|-
 
|-
 
|picard-tools
 
|picard-tools
−
|1.34, 1.73, 1.90
+
|1.34, 1.73
 +
|-
 +
|picard-tools
 +
|1.90
 
|-
 
|-
 
|polyphen
 
|polyphen
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|-
 
|-
 
|python
 
|python
−
|2.6.6, 2.7.3(default), 2.7.3-sqlite, 2.7.5-galaxy, 3.2.3
+
|2.6.6
 +
|-
 +
|python
 +
|2.7.3(default), 2.7.3-sqlite, 3.2.3
 +
|-
 +
|python
 +
|2.7.5-galaxy
 +
|-
 +
|qiime
 +
|1.3.0
 +
|-
 +
|qiime
 +
|1.5.0, 1.6.0
 
|-
 
|-
 
|qiime
 
|qiime
−
|1.3.0, 1.5.0, 1.6.0, 1.7.0
+
|1.7.0
 
|-
 
|-
 
|quake
 
|quake
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|-
 
|-
 
|R
 
|R
−
|2.15.0, 2.15.1, 2.15.2, 3.0.0(default), 3.0.2
+
|2.15.0
 +
|-
 +
|R
 +
|2.15.1, 2.15.2, 3.0.2
 +
|-
 +
|R
 +
|3.0.0(default)
 
|-
 
|-
 
|RAxML
 
|RAxML
Line 455: Line 527:
 
|-
 
|-
 
|samtools
 
|samtools
−
|0.1.16
+
|0.1.16, 0.1.18
−
|-
 
−
|samtools
 
−
|0.1.18
 
 
|-
 
|-
 
|samtools
 
|samtools
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|-
 
|-
 
|smrtanalysis
 
|smrtanalysis
−
|1.4.0
+
|1.4.0, 2.0.1
−
|-
 
−
|smrtanalysis
 
−
|2.0.1
 
 
|-
 
|-
 
|SnpEff
 
|SnpEff
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|-
 
|-
 
|SOAPec
 
|SOAPec
−
|2.01
+
|2.01, 2.02
−
|-
 
−
|SOAPec
 
−
|2.02
 
 
|-
 
|-
 
|SOAPErrorCorrection
 
|SOAPErrorCorrection

Revision as of 00:23, 16 February 2014

Application Installed Version
454 2.6, 2.7
454 2.8
AbundantOTU+ 0.91b
abyss 1.2.5, 1.3.3
abyss 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
bedtools 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
bowtie 1.0.0
bowtie2 2.0.0-beta6, 2.0.2, 2.1.0
bowtie2 2.0.5
breseq 0.24
bwa 0.5.9, 0.7.5a
cafe 2.2
cafe 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, 2.1.1
cufflinks 2.0.2
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, 2.6-4
gatk 2.5-2
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
iprscan 5.45
java 1.6.0_41, 1.7.0_06-i386
java 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
MACS 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
mothur 1.28.0, 1.31.2, 1.32.1
mothur 1.32.0
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, 3.00.01, 3.00.05
novocraft 2.08.03
novocraft 3.00.02
novocraft 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
orthomcl 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
picard-tools 1.90
polyphen 2.2.2
pplacer 1.0, 1.1
prank 121002
prodigal 2.0, 2.2
python 2.6.6
python 2.7.3(default), 2.7.3-sqlite, 3.2.3
python 2.7.5-galaxy
qiime 1.3.0
qiime 1.5.0, 1.6.0
qiime 1.7.0
quake 0.3.4
quast 2.2
quest alpha, devel
R 2.15.0
R 2.15.1, 2.15.2, 3.0.2
R 3.0.0(default)
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
samtools 0.1.19
sam_comp 0.7
SICER 1.1
signalp 4.1
smrtanalysis 1.4.0, 2.0.1
SnpEff 3.2
SnpEff 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)
speciateit template
speciatetest 184
speciate_it 184(default)
sratoolkit 2.1.16
srna-tools 20130118
ssaha2 2.5.5
stacks 0.9996
stacks 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
tophat2 2.0.5
tophat2 2.0.6
tophat2 2.0.7
tophat2 2.0.8
tophat2 2.0.10(default)
treemix 1.12
trf 4.04
trimmomatic 0.22
trimmomatic 0.27
trimmomatic 0.30
trinityrnaseq-intel r2013-02-25
trinityrnaseq r2012-06-08
trinityrnaseq r2013-02-25
trinityrnaseq r2013-08-14
trinotate trinotate_r20130826
truesight 0.06
uchime 4.2.40
usearch 6.0.307
usearch 6.1.544
usearch 7.0.959
USeq 8.5.1
vcftools 0.1.7
vcftools 0.1.11
velvet-kmer245 1.2.10
velvet 1.1.04
velvet 1.2.08
velvet 1.2.10
velvetOptimiser 2.2.5
wessim 1.0
wgs 7.0
wise 2.2.3-rc7
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