#Teaching Lab Shared Server for Sequence Analysis#

##Sept. 2014 - BP205A##

Server: derisilab105.ucsf.edu

• OS: Ubuntu Linux 12 LTS
• RAM: 256Gb
• Cores: 64
• Disk: 7.3 Tb
• Access: use ssh, sftp, or scp to access your account or files. Note, this will require VPN.
• Home Directories: Each team will share an account and home directory, all located in /data/
• Standard shell: zsh
• Shared Data: All shared class data will be stored in: /data/ClassData/

LIST of INSTALLED PACKAGES

(send package or tool install requests to joe AT derisilab.ucsf.edu)

• Programming, graphing, database
  • mysql
  • gcc
  • perl
  • python
  • python-biopython
  • matplotlib
  • numpy
  • scipy
  • pandas (data analysis library for python)
  • gnuplot
• Statistics
  • R
  • python-rpy
• Multiple Sequence Alignment
  • clustalw
  • blast2
  • mafft
  • muscle
• Deep sequence utilities / tools
  • bcftools
  • bowtie2
  • blat
  • bwa
  • gsnap
  • fastx toolkit
  • samtools