abyss=1.9.0 |
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
augustus=3.2.2 |
Y |
|
|
Y |
|
Y |
Y |
|
|
|
Y |
|
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|
|
|
|
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|
|
autoconf=latest |
|
|
Y |
|
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|
|
|
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|
|
|
|
|
|
automake=latest |
|
|
Y |
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|
|
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|
bamtools=2.4.0 |
Y |
|
|
Y |
|
Y |
Y |
Y |
|
|
Y |
|
|
|
|
|
Y |
|
Y |
Y |
|
Y |
bcftools=1.3.1 |
Y |
|
|
Y |
|
Y |
Y |
Y |
|
|
Y |
|
|
|
|
|
Y |
|
Y |
Y |
|
Y |
bedtools=2.25.0 |
Y |
|
|
Y |
|
Y |
Y |
Y |
|
|
Y |
|
|
|
|
|
Y |
|
Y |
Y |
|
Y |
bioconductor-ballgown=2.2.0 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
bioconductor-biobase=2.32.0 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
Y |
bioconductor-biobase=latest |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
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|
|
bioconductor-biocgenerics=latest |
|
Y |
|
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|
|
|
|
|
|
|
|
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|
|
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|
|
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|
bioconductor-biovizbase=1.18.0 |
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
Y |
|
|
|
bioconductor-cummerbund=2.12.1 |
|
|
|
|
|
|
|
|
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|
|
|
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Y |
|
|
bioconductor-cummerbund=2.16.0 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
Y |
|
|
|
bioconductor-dada2=1.0.3 |
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
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|
|
bioconductor-deseq2=1.10.1 |
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
bioconductor-deseq2=1.12.4 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
bioconductor-deseq=1.22.1 |
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
bioconductor-edger=3.14.0 |
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
Y |
Y |
|
|
bioconductor-genomicranges=1.26.1 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
bioconductor-gviz=1.16.5 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
bioconductor-s4vectors=0.12.0 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
blast=2.2.31 |
Y |
|
|
Y |
|
Y |
Y |
|
|
|
Y |
|
|
|
|
|
Y |
|
|
|
|
Y |
blat=35 |
Y |
|
|
Y |
|
Y |
Y |
|
|
|
Y |
|
|
|
|
|
Y |
|
Y |
Y |
|
Y |
bowtie2=2.2.8 |
Y |
|
|
Y |
|
Y |
Y |
Y |
|
|
Y |
|
|
|
|
|
Y |
|
Y |
Y |
|
Y |
bwa=0.7.15 |
Y |
|
|
Y |
|
Y |
Y |
Y |
|
|
Y |
|
|
|
|
|
|
|
|
|
|
Y |
cd-hit=4.6.4 |
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
Y |
|
|
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|
|
circos=0.69.2 |
Y |
|
|
Y |
|
Y |
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
cmake=3.7.1 |
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
cufflinks-patch=2.2.1 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
cufflinks=2.2.1 |
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
Y |
ddocent=2.1 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
deeptools=2.3.2 |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
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|
|
discovar=52488 |
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
discovardenovo=52488 |
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
fastqc=0.11.5 |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
Y |
|
|
|
fastx_toolkit=0.0.14 |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
freebayes=1.0.2.29 |
Y |
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
Y |
gatk=3.5 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
Y |
gatk=3.6 |
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
gcc=latest |
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
genblasta=1.0.4 |
Y |
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
genblastg=1.38 |
Y |
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
hisat2=2.0.4 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
hmmer=3.1b2 |
Y |
|
|
Y |
|
Y |
Y |
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
htseq=0.6.1.post1 |
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
Y |
Y |
|
|
idba=1.1.1 |
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
ipython=latest |
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
jellyfish=2.2.3 |
Y |
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
kallisto=0.43.0 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
Y |
|
|
kat=2.0.8 |
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
kmergenie=1.7016 |
Y |
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
kraken=0.10.6_eaf8fb68 |
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
libgcc=latest |
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
m4=latest |
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
macs2=2.1.1.20160309 |
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
mafft=7.221 |
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
mawk=1.3.4 |
|
|
|
|
|
Y |
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
mcl=14.137 |
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
metaphlan2=2.5.0 |
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
metavelvet-sl-feature-extraction=1.0 |
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
metavelvet-sl=1.0 |
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
metavelvet=1.1.01 |
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
mira=4.0.2 |
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
mothur=1.36.1 |
|
|
|
|
|
Y |
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
multiqc=0.8 |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
numpy=1.11.1 |
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
numpy=latest |
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
pauda=1.0.1 |
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
pear=0.9.6 |
|
|
|
Y |
|
Y |
Y |
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
Y |
perl-app-cpanminus=latest |
Y |
Y |
Y |
Y |
|
|
|
|
|
Y |
|
Y |
|
|
|
|
|
|
|
|
|
Y |
perl-biox-workflow-plugin-filedetails=0.11 |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
|
Y |
|
Y |
|
|
Y |
Y |
Y |
Y |
Y |
Y |
perl-biox-workflow-plugin-fileexists=0.13 |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
|
Y |
Y |
|
Y |
Y |
Y |
Y |
Y |
Y |
perl-biox-workflow=1.10 |
Y |
Y |
|
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
|
Y |
Y |
|
Y |
Y |
Y |
Y |
Y |
Y |
perl-dbi=latest |
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
perl-hpc-runner-command=3.1.1 |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
|
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
perl-termreadkey=latest |
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
picard=2.0.1 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
picard=2.5.0 |
|
|
|
Y |
|
Y |
Y |
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
Y |
prinseq=0.20.4 |
|
|
|
Y |
|
Y |
Y |
|
|
|
|
|
|
|
|
|
|
|
Y |
Y |
|
Y |
pyfaidx=0.4.7.1 |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
pyfasta=0.5.2 |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
pyfastaq=3.11.0 |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
python=2.7 |
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
python=3.5 |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
python=latest |
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
qiime=1.9.1 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
qualimap=2.2.2a |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
quast=4.1 |
|
|
|
Y |
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
r-base=3.3.1 |
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
Y |
|
|
Y |
r-cairo=latest |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
r-essentials=latest |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
Y |
|
|
Y |
r-ggplot2=latest |
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
r=3.3.1 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
rainbow=2.0.4 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
repeatmasker=4.0.6 |
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
rmblast=2.2.28 |
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
rsem=1.2.28 |
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
salmon=0.6.0 |
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
samtools=1.3.1 |
Y |
|
|
Y |
|
Y |
Y |
Y |
|
|
Y |
|
|
|
|
|
Y |
|
Y |
Y |
|
Y |
scipy=latest |
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
seqtk=1.2 |
|
|
|
Y |
|
Y |
Y |
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|
Y |
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|
Y |
|
Y |
Y |
|
Y |
sickle=0.5 |
|
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|
Y |
|
|
Y |
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snpeff=4.3 |
Y |
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Y |
snpsift=4.3 |
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Y |
soapdenovo2-gapcloser=1.12 |
|
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Y |
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soapdenovo2-prepare=2.0 |
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Y |
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soapdenovo2=2.40 |
|
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Y |
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spades=3.9.0 |
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Y |
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stacks=1.40 |
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Y |
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star=2.5.2a |
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Y |
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Y |
Y |
|
Y |
stringtie=1.3.0 |
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Y |
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tophat=2.1.0 |
Y |
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Y |
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Y |
Y |
|
Y |
transdecoder=2.1.0 |
Y |
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Y |
|
trimmomatic=0.35 |
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Y |
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|
trimmomatic=0.36 |
|
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Y |
|
Y |
Y |
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|
Y |
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Y |
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trinity=2.2.0 |
|
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Y |
|
trinotate=3.0.1 |
Y |
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Y |
|
vcflib=1.0.0_rc1 |
Y |
|
|
Y |
|
Y |
Y |
Y |
|
|
Y |
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|
|
Y |
|
Y |
Y |
|
Y |
vcftools=0.1.14 |
Y |
|
|
Y |
|
Y |
Y |
Y |
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|
Y |
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|
Y |
|
Y |
Y |
|
Y |
velvet=1.2.10 |
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Y |
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zlib=latest |
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Y |
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