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=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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