I am trying to get the latest version of breakDancer running on our local hardware When using the instructions in Install.md I am encountering as below. First I receive an error from the cmake step where it appears the test for breakDancer-max is missing somehow If I ignore this error and proceed with the make there are problems with boost (it appears as though it is looking in the wrong place for bootstrap.sh) I have had good luck for the most part with the pre-compiled breakdancer 1.1.2 off http://gmt.genome.wustl.edu/breakdancer/current/ however I have never been able to get the -o option to work so was hoping that this would be resolved in the latest version. Any help is appreciated (I have spent hours trying to get this installed and am a bit at wits end)

/home/tools/CNV/genome/pem/Breakdancer> git clone --recursive https://github.com/genome/breakdancer.git Initialized empty Git repository in /home/tools/CNV/genome/pem/Breakdancer/breakdancer/.git/ remote: Counting objects: 3520, done. remote: Compressing objects: 100% (1485/1485), done. remote: Total 3520 (delta 1578), reused 3520 (delta 1578) Receiving objects: 100% (3520/3520), 8.38 MiB | 1.34 MiB/s, done. Resolving deltas: 100% (1578/1578), done. Submodule 'build-common' (git://github.com/genome/build-common.git) registered for path 'build-common' Initialized empty Git repository in /home/tools/CNV/genome/pem/Breakdancer/breakdancer/build-common/.git/ remote: Reusing existing pack: 175, done. remote: Total 175 (delta 0), reused 0 (delta 0) Receiving objects: 100% (175/175), 1.98 MiB | 94 KiB/s, done. Resolving deltas: 100% (63/63), done. Submodule path 'build-common': checked out '28f2df445cddd7c09c09d79d3d30bddd458da223' export SAMTOOLS_ROOT=/home/tools/CNV/genome/pem/Breakdancer/samtools-0.1.19/ /home/tools/CNV/genome/pem/Breakdancer> cd breakdancer /home/tools/CNV/genome/pem/Breakdancer/breakdancer> mkdir build /home/tools/CNV/genome/pem/Breakdancer/breakdancer> cd build /home/tools/CNV/genome/pem/Breakdancer/breakdancer/build> cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local -- The C compiler identification is unknown -- The CXX compiler identification is unknown -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done Score floating point type: double -- Looking for include files CMAKE_HAVE_PTHREAD_H -- Looking for include files CMAKE_HAVE_PTHREAD_H - found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE Extracting boost from /home/tools/CNV/genome/pem/Breakdancer/breakdancer/vendor/boost-1.54-breakdancer.tar.gz Boost build log can be found at /home/tools/CNV/genome/pem/Breakdancer/breakdancer/build/vendor/boost-src/build.log -- Configuring done CMake Error at build-common/cmake/TestHelper.cmake:65 (add_test): Error evaluating generator expression:

$<TARGET_FILE:breakdancer-max>

No target "breakdancer-max" Call Stack (most recent call first): integration-test/CMakeLists.txt:3 (def_integration_test)

-- Generating done -- Build files have been written to: /home/tools/CNV/genome/pem/Breakdancer/breakdancer/build

/home/tools/CNV/genome/pem/Breakdancer/breakdancer/build> make Scanning dependencies of target boost-1.54 [-12%] Creating directories for 'boost-1.54' [-12%] Performing download step (verify and extract) for 'boost-1.54' -- verifying file... file='/home/tools/CNV/genome/pem/Breakdancer/breakdancer/vendor/boost-1.54-breakdancer.tar.gz' -- verifying file... warning: did not verify file - no URL_MD5 checksum argument? corrupt file? -- extracting... src='/home/tools/CNV/genome/pem/Breakdancer/breakdancer/vendor/boost-1.54-breakdancer.tar.gz' dst='/home/tools/CNV/genome/pem/Breakdancer/breakdancer/build/vendor/boost-src' -- extracting... [tar xfz] -- extracting... [analysis] -- extracting... [rename] -- extracting... [clean up] -- extracting... done [-12%] No patch step for 'boost-1.54' [-12%] No update step for 'boost-1.54' [-12%] Performing configure step for 'boost-1.54' /bin/sh: ./bootstrap.sh: No such file or directory make[2]: * [vendor/src/boost-1.54-stamp/boost-1.54-configure] Error 127 make[1]: [CMakeFiles/boost-1.54.dir/all] Error 2 make: ** [all] Error 2