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, off campus will require VPN. In the teaching lab, the network “TeachingLab” should let you in. Password is written on the router.
• 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