Build Breakdancer Fails

Question

[m.kooijman]

Im trying to build latest versions of breakdancer under ubuntu 12.04, cmake version 2.8.7, GCC 4.6.3.However, it fails. i'm following the exact steps as described on git (https://github.com/genome/breakdancer/blob/master/INSTALL.md)

git clone --recursive https://github.com/genome/breakdancer.git
cd breakdancer
mkdir build
cd build/
wget "http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2"
tar -jxvf samtools-0.1.19.tar.bz2
cd samtools-0.1.19
make
export SAMTOOLS_ROOT=$(pwd)
cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local

However it fails.

-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- 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
CMake Error at CMakeLists.txt:20 (include):
  include could not find load file:

    TestHelper


CMake Error at CMakeLists.txt:21 (include):
  include could not find load file:

    VersionHelper


CMake Error at CMakeLists.txt:22 (include):
  include could not find load file:

    ProjectHelper


Extracting boost from /home/username/breakdancer/vendor/boost-1.54-breakdancer.tar.gz
Boost build log can be found at /home/username/breakdancer/build/vendor/boost-src/build.log
CMake Error at CMakeLists.txt:52 (add_projects):
  Unknown CMake command "add_projects".

-- Configuring incomplete, errors occurred!

Since I do not have little to non experience with Cmake, I do not know where to start to remove this error.

Answer 1

[ernfrid]

Both of those errors seem to indicate that the build_common submodule did not come down when you cloned breakdancer from github. You might want to attempt to clone again, and then verify that the build-common subdirectory has files within it after you clone.

Also, you no longer need to hassle with compiling samtools by hand. The repository should come with boost and samtools included. I have updated INSTALL.md to indicate this.

[m.kooijman]

It was a firewall problem: changing from git to https worked using : git config --global url."https://".insteadOf git://

[ernfrid]

Thanks for reporting what change worked. I've updated the repository to use https for build-common instead of git.

[sjmilleruaz]

Using git clone https://github.com/genome/breakdancer.git does not get the build-common directory contents. In order to build breakdancer 1.4.4 I had to also do git clone https://github.com/genome/build-common.git While it does compile, the make install output lists the lib directory as breakdancer-max1.4.4-unstable-1.17bbb34-dirty/ I'm not sure I trust something named "unstable...dirty" It also appears that the README file has not been updated since version 1.3.6 This doesn't inspire much confidence in the software.