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* Note: Used mdiutil to turn off Spotlight; might need to reenable it. = Upgrade Plan 10-31-14= * 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= * 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= ==OS== * MacOS X 10.5 Leopard (Will soon upgrade to Snow Leopard) ==MacPorts== * 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== * 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== * 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=== * BWA * SOAPdeNovo (Need to upgrade to Snow Leopard * Stampy (Need to upgrade python)
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