Trouble Installing Breakdancer 1.4.2: Boost Libraries Inexplicably Not Visible

Question

[tptacek3050]

I am attempting to install Breakdancer 1.4.2 on a 64 bit Linux CentOS 5.6 cluster. I do not have root access: I'm am installing my own personal copy. I have been following the installation instructions as shown here: https://github.com/genome/breakdancer/blob/master/INSTALL.md.

I get to this step:

cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local

And I get the following output:

=====================

Score floating point type: double -- Found Samtools - Samtools include dirs: /share/apps/ngs-ccts/breakdancer-1.4.2/breakdancer/build/samtools-0.1.19;/usr/include - Samtools libraries: /share/apps/ngs-ccts/breakdancer-1.4.2/breakdancer/build/samtools-0.1.19/libbam.a;/usr/lib64/libz.so CMake Error at /share/apps/cmake/cmake-2.8.10.2-Linux-i386/share/cmake-2.8/Modules/FindBoost.cmake:1192 (message): Unable to find the requested Boost libraries.

Boost version: 1.52.0

Boost include path: /share/apps/ngs-ccts/boost_1_52_0

The following Boost libraries could not be found:

      boost_system
      boost_chrono

Some (but not all) of the required Boost libraries were found. You may need to install these additional Boost libraries. Alternatively, set BOOST_LIBRARYDIR to the directory containing Boost libraries or BOOST_ROOT to the location of Boost. Call Stack (most recent call first): CMakeLists.txt:28 (find_package)

-- Configuring incomplete, errors occurred!

===================

However, in the /share/apps/ngs-ccts/boost_1_52_0/libs folder there are folders called system/ and chrono/ which I presume have the missing libraries in them. Is there a way I can redirect the compiler to the correct directories? Is this indicative of an error in the way Boost was installed on the cluster (i.e. do I need to call my tech support guys)?

Travis Ptacek

[Dan D]

What do you see when you type echo $BOOST_LIBRARYDIR and echo $BOOST_ROOT?

[tptacek3050]

I get blank lines.

[Dan D]

can you do this and try again?: export BOOST_LIBRARYDIR=/share/apps/ngs-ccts/boost_1_52_0/libs export BOOST_ROOT=/share/apps/ngs-ccts/boost_1_52_0/

[tptacek3050]

Just tried it, I get the same error message.

[Dan D]

try typing yum install boost and then retry the installation.

[tptacek3050]

I need to be root (not possible for me) to perform this command. Do I need to contact the cluster administrators?

[Dan D]

Oops, I totally missed that in your initial post. Yes, I would contact the cluster administrators at this point. All of the other ideas I have would require you to be root.

[tptacek3050]

What should I tell him? Is boost not installed correctly? Do I need to get him to install the software for me?

[Dan D]

I would ask him to do a yum install boost. That's easy for him and likely to work for your app. If he balks, I would then explain that you tried to point your app to the specific path of the boost libs via setting specific environment variables, but that it didn't work and is indicative of a boost library installation that would also not suffice for other applications folks might want to install in the future.

Answer 1

[tgi.tabbott]

Hello. I just pushed a new version to master that includes the required parts of boost. If you update (git pull) from github, or simply reclone the repository, you should be able to proceed without having to explicitly install boost.

[tptacek3050]

Just tried running it this morning and it worked. Thanks!