Genome Miner Reinstall

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  • Note: Used mdiutil to turn off Spotlight; might need to reenable it.

Upgrade Plan 10-31-14[edit]

Hardware[edit]

  • Three internal drives:
    • Macintosh HD, mounted at /, 2 TB
    • FreshReads, mounted at /Volumes/FreshReads, 2 TB
    • DataDrive, mounted at /Volumes/DataDrive, 4 TB RAID 0
  • Two external drives:
    • Buffalo External, mounted at /Volumes/Ext4T, 4 TB RAID 0
    • Silver External, mounted at /Volumes/Ext8T, 8 TB RAID 0

Software[edit]

OS[edit]

  • MacOS X 10.5 Leopard (Will soon upgrade to Snow Leopard)

MacPorts[edit]

  • MacPorts installed in /opt/local/
    • If you need to install a UNIX/Linux program, see if a Mac Port is available here: http://www.macports.org/ports.php
    • You can install it using "sudo port install PACKAGENAME"
  • Software installed through MacPorts:
    • ImageMagick
    • FFTW
    • gnuplot
    • FFTW
    • Ghostscript
    • xsltproc
    • XML::Simple
    • zlib, bzlib

Illumina Pipeline[edit]

  • OLB 1.8 is installed at /Users/ajgore/Desktop/OLB-1.8.0
    • SPECIAL NOTE: Changed the source code of OLB in a few places.
      • OLB will fail to compile. It will complain of an unknown type uint.
      • The problem files are in c++/common: Alignment.cpp, cppunit/testSequence.cpp, Sequence.cpp, and Sequence.hh
      • Enter these files, and replace "uint" with "unsigned int"; OLB will then compile properly.
      • Most files have a "typedef uint unsigned int" at the top; these four do not

Bioinformatics Software[edit]

  • Currently installed at /Users/kunzhang/softwares:
  • Bowtie
  • Soap (Mapper)
    • SPECIAL NOTE: To compile soap, I needed to remove the "-static" flag from the RELEASE_FLAGS and STATIC_FLAGS lines in the Makefile. This forces soap to compile as a dynamically linked program, as MacOS does not support static linking in this manner
  • ABySS
    • SPECIAL NOTE: To compile ABySS, use the following command: ./configure CXX=g++-4.2 CPPFLAGS="-arch x86_64" LDFLAGS="-arch x86_64" && make AM_CXXFLAGS='-Wall -Wextra'
  • Samtools
    • SPECIAL NOTE: When compiling Samtools, we must force a 64-bit architechture. Change the makefile so that line 2 is now:
      • CFLAGS= -g -Wall -O2 -arch x86_64 #-m64 #-arch ppc
      • LDFLAGS= -arch x86_64
  • Picard
    • Should work, since it uses Java
  • GATK
    • Should work, since it uses Java

Still to Install[edit]

  • BWA
  • SOAPdeNovo (Need to upgrade to Snow Leopard
  • Stampy (Need to upgrade python)