NBIC Galaxy Server: Current Tools
From BioAssist
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 |
