Question: Build Breakdancer Fails
0
gravatar for m.kooijman
3.7 years ago by
m.kooijman0
m.kooijman0 wrote:

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.

breakdancer • 2.1k views
ADD COMMENTlink modified 2.0 years ago by Biostar ♦♦ 20 • written 3.7 years ago by m.kooijman0
0
gravatar for ernfrid
3.7 years ago by
ernfrid380
Saint Louis
ernfrid380 wrote:

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.

ADD COMMENTlink written 3.7 years ago by ernfrid380

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

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by m.kooijman0

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

ADD REPLYlink written 3.7 years ago by ernfrid380

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.

ADD REPLYlink written 3.5 years ago by sjmilleruaz0
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