NBIC Galaxy Server: Current Tools

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On each distribution of the NBIC Galaxy server (e.g. on line version or VMs), only one version of a tool/library exists.

Below is a list of tools/libraries installed at the Galaxy server.

Name Version Installed location Remark
Bowtie 0.12.7 /mnt/galaxyTools/tools/bowtie
Cufflinks 1.1.0 /mnt/galaxyTools/tools/cufflinks
Samtools 0.1.12 /mnt/galaxyTools/tools/samtools
Tophat 1.3.3 /mnt/galaxyTools/tools/tophat
R 2.15.2 /usr/bin/R
Gnuplot 4.4.0 /usr/bin/gnuplot A default debian package
liftOver 2012-07-24 /mnt/galaxyTools/tools/ucsc_tools
Stampy 1.0.20 /usr/local/galaxytools/stampy wrapper only supports several parameters.
Velvet 1.2.08 /mnt/galaxyTools/tools/velvet compiled with "make 'OPENMP=1' 'CATEGORIES=5' 'MAXKMERLENGTH=64' 'BIGASSEMBLY=1' velvetg velveth"
ABySS 1.3.4 /usr/local/galaxytools/abyss Debian package is not complete. So built from source.
BWA 0.5.7 /mnt/galaxyTools/tools/bwa only support hg19
Perm 3.0 /mnt/galaxyTools/tools/perm only support hg19
gmap/gsnap 2012-07-20 /usr/local/galaxytools/gmap only support hg19, seed size 12-15
GATK 1.2 /mnt/galaxyTools/tools/gatk
BLAST 2.2.22 /mnt/galaxyTools/tools/gatk
macs 1.3.7.1 /mnt/galaxyTools/tools/macs
mosaik 1.1 /mnt/galaxyTools/tools/mosaik
plink 1.07 /mnt/galaxyTools/tools/plink
bfast 0.7.0a /mnt/galaxyTools/tools/bfast
MAQ 0.7.1 /mnt/galaxyTools/tools/maq
Picard 1.55 /mnt/galaxyTools/tools/picard
srma 0.1.15 /mnt/galaxyTools/tools/srma