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]
- New internal hybrid drives, 4TBx2
- Plan to replace current root drive on MacPro/Genome-miner
- Step 1: Mount the 4TB drive in an external enclosure and use Mac disk utility to format and create a 500 GB partition. Do this on both 4TB disks, one carrying a copy of the current Genome-miner set up (Ubuntu backup + MacOs X backup) and another new drive for fresh Ubuntu install.
- Step 2: Clone MacHD (MacOS X) into the 500 GB partition (following these steps: http://nyacomputing.com/how-to-create-a-bootable-clone-of-your-mac-hard-drive/)
- Step 3: Install Ubuntu fresh into the leftover 3TB space for dual-boot (follow these steps: https://help.ubuntu.com/community/MactelSupportTeam/AppleIntelInstallation)
- Step 4: Switch out old hard drive for new 4TB hard drive
- Set up automatic security updates: http://www.howtogeek.com/204796/how-to-enable-automatic-security-updates-on-ubuntu-server/
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
- SPECIAL NOTE: Changed the source code of OLB in a few places.
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
- SPECIAL NOTE: When compiling Samtools, we must force a 64-bit architechture. Change the makefile so that line 2 is now:
- 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)