====== Virtual server for applications (Ubuntu 12.04 - code name RachaelX) ======

  * [[rachaelx:bases|Install base system]]
  * [[rachaelx:qiime|Install QIIME (1.5.0)]]
  * [[rachaelx:qiimefix|Fix Qiime installation test errors (1.5.0)]]
  * [[rachaelx:trinity|Install Trinity]]
  * [[rachaelx:blastl|Install Blast+ and Blast legacy]]
  * [[rachaelx:bioperl|Install bioperl]]
  * [[rachaelx:qiime160|Install QIIME (1.6.0)]]
  * [[rachaelx:mira399|Install Mira from source (3.9.9)]]
  * [[rachaelx:mira3910|Update Mira from source (3.9.10/3.9.11/3.9.18)]]
  * [[rachaelx:mira3rd|Mira 3rd party tools]]
  * [[rachaelx:sanger1|SMALT and SSAHA2]]
  * [[rachaelx:tophat|Tophat (1.4.1 from binary)]]
  * [[rachaelx:erre|R, RStudio server and Bioconductor]]
  * [[rachaelx:qiime170|Install QIIME (1.7.0)]]
  * [[rachaelx:pandaseq|Install Pandaseq]]
  * [[rachaelx:wgs|WGS-assembler]]
  * [[rachaelx:amos|AMOS]]
  * [[rachaelx:mummer|MUMmer]]
  * [[rachaelx:bwa|BWA]]
  * [[rachaelx:blasr|BLASR]]
  * [[rachaelx:hmmer|HMMER]]
  * [[rachaelx:uptrinityrsem|Upgrade Trinity + RSEM]]
  * [[rachaelx:trinotate|Trinotate]]
  * [[rachaelx:uptrinity202|Upgrade Trinity 2.0.2]]
  * [[rachaelx:bowtop2|Bowtie2 & Tophat2 (from binary)]]