Problem compiling bcl2fastq-1.8.4

[emixaM]

Hello!

I am trying to compile bcl2fastq on a server where I cannot be root and should be installed in a specific folder (server is under CentOS 6.5).

I followed the manual's insctructions.

First I downloaded the tarball:

wget ftp://webdata:[email protected]/Downloads/Software/bcl2fastq/bcl2fastq-1.8.4.tar.bz2

Then created some variables:

export TMP=/tmp
export SOURCE=${TMP}/bcl2fastq-1.8.4
export BUILD=${TMP}/bcl2fastq-1.8.4-build
export INSTALL=/software/bcl2fastq/bcl2fastq-1.8.4

Then I extracted the files:

cd ${TMP}
tar xjf /software/bcl2fastq/bcl2fastq-1.8.4.tar.bz2
mv bcl2fastq bcl2fastq-1.8.4

Then I ran the configuration:

mkdir ${BUILD}
cd ${BUILD}
${SOURCE}/src/configure --prefix=${INSTALL}

But at this step I encounter an error, at 93% of the compilation :

Linking CXX executable ../bin/ccmake
/software6/apps/buildtools/20140527/bin/ld: CMakeFiles/ccmake.dir/CursesDialog/cmCursesMainForm.o: undefined reference to symbol 'keypad'
/lib64/libtinfo.so.5: error adding symbols: DSO missing from command line

Do you have any idea to solve the problem?

Cheers!

[GenoMax]

https://www.centos.org/forums/viewtopic.php?t=6469.

See if this works:

$ export LDFLAGS="$LDFLAGS -ltinfo"

and recompile.

[emixaM]

TIP OF THE HAT to you!

The compilation could get going.

A new hurdle has come, with Boost.

At the end of the compilation, I can see that Boost has been successfully installed:

boost-1_44_0 installed successfully
-- Successfuly built boost 1.44.0 from the distribution package...

But few lines down:

CMake Error at /tmp/bcl2fastq-1.8.4-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:1128 (message):
  Unable to find the requested Boost libraries.

  Boost version: 1.44.0

  Boost include path: /tmp/bcl2fastq-1.8.4-build/opt/bootstrap/include

  The following Boost libraries could not be found:

          boost_thread

  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.

I found this : http://stackoverflow.com/questions/1...-finding-boost

So I am trying to recompile using --static parameter of configure.

[emixaM]

New stop on the compilation :

...
-- All libraries will be statically linked
-- Found ZLIB  header: /usr/include/zlib.h
-- Found ZLIB library: /usr/lib64/libz.a
-- gzip compression supported
CMake Error at cmake/cxxConfigure.cmake:84 (message):
  No support for bzip2 compression

I found other threads with the similar problem, but when installing on Ubuntu.
I have bzip2 installed:

$ rpm -qa | grep bzip
bzip2-1.0.5-7.el6_0.x86_64
bzip2-libs-1.0.5-7.el6_0.x86_64
bzip2-devel-1.0.5-7.el6_0.x86_64
$ ls -lh /usr/lib64/libbz2.so 
lrwxrwxrwx 1 root root 23 28 oct.  10:55 /usr/lib64/libbz2.so -> ../../lib64/libbz2.so.1

How can I make the configure script to see it?

[GenoMax]

Can you add /lib64 to LD_LIBRARY_PATH and try re-compiling?

[emixaM]

I did :

$ export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/lib64"

Then :

$ ${SOURCE}/src/configure --prefix=${INSTALL} --static

But :

CMake Error at cmake/cxxConfigure.cmake:84 (message):
  No support for bzip2 compression

Should I delete the building folder to re-compile? Because it went straight to the Boost compilation :

cmake version "cmake version 2.8.4" is already installed at /tmp/bcl2fastq-1.8.4-build/bootstrap/bin/cmake
nothing to be done
Using installed /tmp/bcl2fastq-1.8.4-build/bootstrap/bin/cmake

[GenoMax]

Do a "make clean" and try again. I have a feeling it is not going to help.

Probably pretty late in France so we can take this up tomorrow in case no one else comes along with a brilliant answer between now and tomorrow.

[emixaM]

I moved to Canada, and forgot to update the details!

Currently re-compiling...

[emixaM]

...and it did not work.

[GenoMax]

Let me think some more (till later this evening). If you manage to complete the compilation in the meanwhile post an update.

[sklages]

Do you find a

/usr/include/bzlib.h

just like you find the header for the gzip compression?

[emixaM]

Actually I am just at the step of the configure script. I am trying to solve the libraries links. I am sure that it is not the bzip2 library that is problematic here, but something with boost thread and GCC version. I will keep you updated.

[GenoMax]

What version of gcc are you using?

[sklages]

What version of gcc are you using?

Good point, I had severe problems compiling with gcc 4.7.1 due to some issues in combination with boost 1.44 ..

[emixaM]

I tried the oldest gcc on my system, it did not work :

C compiler on this system is: /compilers/gcc/4.6/bin/gcc 
C++ compiler on this system is: /compilers/gcc/4.6/bin/g++

And in the end :

CMake Error at cmake/cxxConfigure.cmake:84 (message):
  No support for bzip2 compression