Virtual server for applications (Ubuntu 12.04 - code name RachaelX)
Install base system
Install QIIME (1.5.0)
Fix Qiime installation test errors (1.5.0)
Install Trinity
Install Blast+ and Blast legacy
Install bioperl
Install QIIME (1.6.0)
Install Mira from source (3.9.9)
Update Mira from source (3.9.10/3.9.11/3.9.18)
Mira 3rd party tools
SMALT and SSAHA2
Tophat (1.4.1 from binary)
R, RStudio server and Bioconductor
Install QIIME (1.7.0)
Install Pandaseq
WGS-assembler
AMOS
MUMmer
BWA
BLASR
HMMER
Upgrade Trinity + RSEM
Trinotate
Upgrade Trinity 2.0.2
Bowtie2 & Tophat2 (from binary)