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Old 12-17-2014, 09:18 AM   #1
emixaM
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Default Problem compiling bcl2fastq-1.8.4

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:

Code:
wget ftp://webdata:webdata@ussd-ftp.illumina.com/Downloads/Software/bcl2fastq/bcl2fastq-1.8.4.tar.bz2
Then created some variables:

Code:
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:

Code:
cd ${TMP}
tar xjf /software/bcl2fastq/bcl2fastq-1.8.4.tar.bz2
mv bcl2fastq bcl2fastq-1.8.4
Then I ran the configuration:
Code:
mkdir ${BUILD}
cd ${BUILD}
${SOURCE}/src/configure --prefix=${INSTALL}
But at this step I encounter an error, at 93% of the compilation :
Code:
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!
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Old 12-17-2014, 09:37 AM   #2
GenoMax
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https://www.centos.org/forums/viewtopic.php?t=6469.

See if this works:

Code:
$ export LDFLAGS="$LDFLAGS -ltinfo"
and recompile.
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Old 12-17-2014, 10:13 AM   #3
emixaM
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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:

Code:
boost-1_44_0 installed successfully
-- Successfuly built boost 1.44.0 from the distribution package...
But few lines down:

Code:
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.
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Old 12-17-2014, 10:35 AM   #4
emixaM
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New stop on the compilation :

Code:
...
-- 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:

Code:
$ 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?

Last edited by emixaM; 12-17-2014 at 10:50 AM.
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Old 12-17-2014, 10:52 AM   #5
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Can you add /lib64 to LD_LIBRARY_PATH and try re-compiling?
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Old 12-17-2014, 11:27 AM   #6
emixaM
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I did :

Code:
$ export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/lib64"
Then :

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

Code:
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 :

Code:
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
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Old 12-17-2014, 11:48 AM   #7
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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.
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Old 12-17-2014, 11:53 AM   #8
emixaM
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I moved to Canada, and forgot to update the details!

Currently re-compiling...
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Old 12-17-2014, 11:57 AM   #9
emixaM
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...and it did not work.
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Old 12-17-2014, 12:00 PM   #10
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Let me think some more (till later this evening). If you manage to complete the compilation in the meanwhile post an update.
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Old 12-17-2014, 01:01 PM   #11
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Do you find a
Quote:
/usr/include/bzlib.h
just like you find the header for the gzip compression?
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Old 12-17-2014, 01:23 PM   #12
emixaM
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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.
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Old 12-17-2014, 02:09 PM   #13
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What version of gcc are you using?
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Old 12-17-2014, 10:58 PM   #14
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Quote:
Originally Posted by GenoMax View Post
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 ..
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Old 12-18-2014, 05:09 AM   #15
emixaM
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I tried the oldest gcc on my system, it did not work :

Code:
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 :

Code:
CMake Error at cmake/cxxConfigure.cmake:84 (message):
  No support for bzip2 compression
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Old 12-18-2014, 09:07 AM   #16
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With a clean install :

Code:
Decompressing /tmp/bcl2fastq-1.8.4/src/../redist/cmake-2.8.4.tar.gz
---------------------------------------------
CMake 2.8.4, Copyright 2000-2009 Kitware, Inc.
C compiler on this system is: /compilers/gcc/4.5/bin/gcc 
C++ compiler on this system is: /compilers/gcc/4.5/bin/g++ 
Makefile processor on this system is: gmake
/compilers/gcc/4.5/bin/g++ is GNU compiler
/compilers/gcc/4.5/bin/g++ has STL in std:: namespace
/compilers/gcc/4.5/bin/g++ has ANSI streams
/compilers/gcc/4.5/bin/g++ has streams in std:: namespace
/compilers/gcc/4.5/bin/g++ has sstream
/compilers/gcc/4.5/bin/g++ has operator!=(string, char*)
/compilers/gcc/4.5/bin/g++ has stl iterator_traits
/compilers/gcc/4.5/bin/g++ has standard template allocator
/compilers/gcc/4.5/bin/g++ has allocator<>::rebind<>
/compilers/gcc/4.5/bin/g++ does not have non-standard allocator<>::max_size argument
/compilers/gcc/4.5/bin/g++ has stl containers supporting allocator objects
/compilers/gcc/4.5/bin/g++ has header cstddef
/compilers/gcc/4.5/bin/g++ requires template friends to use <>
/compilers/gcc/4.5/bin/g++ supports member templates
/compilers/gcc/4.5/bin/g++ has standard template specialization syntax
/compilers/gcc/4.5/bin/g++ has argument dependent lookup
/compilers/gcc/4.5/bin/g++ has struct stat with st_mtim member
/compilers/gcc/4.5/bin/g++ has ios::binary openmode
/compilers/gcc/4.5/bin/g++ has ANSI for scoping
---------------------------------------------
...
Cleaning up /tmp/bcl2fastq-1.8.4-build/bootstrap/build/cmake-2.8.4
CMake installed successfully
Using installed /tmp/bcl2fastq-1.8.4-build/bootstrap/bin/cmake
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /compilers/gcc/4.5/bin/gcc
-- Check for working C compiler: /compilers/gcc/4.5/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /compilers/gcc/4.5/bin/g++
-- Check for working CXX compiler: /compilers/gcc/4.5/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- install      prefix: /software/bcl2fastq/bcl2fastq-1.8.4
-- install exec prefix: .
-- install     bin dir: ./bin
-- install     lib dir: ./lib/bcl2fastq-1.8.4
-- install libexec dir: ./libexec/bcl2fastq-1.8.4
-- install include dir: include/bcl2fastq-1.8.4
-- install    data dir: share/bcl2fastq-1.8.4
-- install     doc dir: doc/bcl2fastq-1.8.4
-- install     man dir: man
-- Verifying target directories access
-- Creating external tools in subdirectory opt
-- Could NOT find Boost
-- Boost 1.44.0 not found. Boost will be built from the distribution...
Decompressing /tmp/bcl2fastq-1.8.4/src/../redist/boost_1_44_0.tar.gz
Building Boost.Jam with toolset gcc... tools/jam/src/bin.linuxx86_64/bjam
Unicode/ICU support for Boost.Regex?... not found.
Generating Boost.Build configuration in project-config.jam...

Bootstrapping is done. To build, run:

    ./bjam
    
To adjust configuration, edit 'project-config.jam'.
Further information:

   - Command line help:
     ./bjam --help
     
   - Getting started guide: 
     http://www.boost.org/more/getting_started/unix-variants.html
     
   - Boost.Build documentation:
     http://www.boost.org/boost-build2/doc/html/index.html

...found 14 targets...
...updating 8 targets...
common.mkdir bin.v2
common.mkdir bin.v2/libs
common.mkdir bin.v2/libs/regex
common.mkdir bin.v2/libs/regex/build
common.mkdir bin.v2/libs/regex/build/gcc-4.5.4
common.mkdir bin.v2/libs/regex/build/gcc-4.5.4/debug
gcc.compile.c++ bin.v2/libs/regex/build/gcc-4.5.4/debug/has_icu_test.o
libs/regex/build/has_icu_test.cpp:12:30: erreur fatale: unicode/uversion.h : Aucun fichier ou dossier de ce type
compilation terminée.

    "g++"  -ftemplate-depth-128 -O0 -fno-inline -Wall -g -fPIC  -DBOOST_ALL_NO_LIB=1 -DBOOST_HAS_ICU=1  -I"." -c -o "bin.v2/libs/regex/build/gcc-4.5.4/debug/has_icu_test.o" "libs/regex/build/has_icu_test.cpp"

...failed gcc.compile.c++ bin.v2/libs/regex/build/gcc-4.5.4/debug/has_icu_test.o...
...skipped <pbin.v2/libs/regex/build/gcc-4.5.4/debug>has_icu for lack of <pbin.v2/libs/regex/build/gcc-4.5.4/debug>has_icu_test.o...
...failed updating 1 target...
...skipped 1 target...
...updated 6 targets...
Performing configuration checks

    - has_icu builds           : no

Component configuration:

    - date_time                : building
    - filesystem               : building
    - graph                    : not building
    - graph_parallel           : not building
    - iostreams                : building
    - math                     : not building
    - mpi                      : not building
    - program_options          : building
    - python                   : not building
    - random                   : not building
    - regex                    : building
    - serialization            : building
    - signals                  : not building
    - system                   : building
    - test                     : not building
    - thread                   : building
    - wave                     : not building

...patience...
...
...patience...
...found 17154 targets...
...updating 8274 targets...
...
...updated 8274 targets...
boost-1_44_0 installed successfully
-- Successfuly built boost 1.44.0 from the distribution package...
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for floorf
-- Looking for floorf - found
-- Looking for round
-- Looking for round - found
-- Looking for roundf
-- Looking for roundf - found
-- Looking for powf
-- Looking for powf - found
-- Looking for erf
-- Looking for erf - found
-- Looking for erf
-- Looking for erf - found
-- Looking for erfc
-- Looking for erfc - found
-- Looking for erfc
-- Looking for erfc - found
-- 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
Call Stack (most recent call first):
  c++/CMakeLists.txt:33 (include)


-- Configuring incomplete, errors occurred!
But again:

Code:
$ 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
Any ideas?
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Old 12-18-2014, 09:56 AM   #17
emixaM
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Oh, I removed the --static and it went through O_o

Let's go to the make, now...
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Old 12-18-2014, 11:33 AM   #18
emixaM
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make and make install worked flawlessly

BUT...

When launching the executable, I encountered the well documented problem:

Code:
$ ./configureBclToFastq.pl
"my" variable $value masks earlier declaration in same statement at /software/bcl2fastq/bcl2fastq-1.8.4/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 760.
syntax error at /software/bcl2fastq/bcl2fastq-1.8.4/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 747, near "$variable qw(ELAND_FASTQ_FILES_PER_PROCESS)"
Global symbol "$variable" requires explicit package name at /software/bcl2fastq/bcl2fastq-1.8.4/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 749.
syntax error at /software/bcl2fastq/bcl2fastq-1.8.4/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 751, near "$directory qw(ELAND_GENOME)"
Global symbol "$self" requires explicit package name at /software/bcl2fastq/bcl2fastq-1.8.4/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
Global symbol "$directory" requires explicit package name at /software/bcl2fastq/bcl2fastq-1.8.4/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
Global symbol "$project" requires explicit package name at /software/bcl2fastq/bcl2fastq-1.8.4/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
Global symbol "$sample" requires explicit package name at /software/bcl2fastq/bcl2fastq-1.8.4/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
Global symbol "$lane" requires explicit package name at /software/bcl2fastq/bcl2fastq-1.8.4/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
Global symbol "$barcode" requires explicit package name at /software/bcl2fastq/bcl2fastq-1.8.4/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
Global symbol "$reference" requires explicit package name at /software/bcl2fastq/bcl2fastq-1.8.4/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
syntax error at /software/bcl2fastq/bcl2fastq-1.8.4/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 761, near "}"
/software/bcl2fastq/bcl2fastq-1.8.4/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm has too many errors.
Compilation failed in require at /software/bcl2fastq/bcl2fastq-1.8.4/lib/bcl2fastq-1.8.4/perl/Casava/Alignment.pm line 61.
BEGIN failed--compilation aborted at /software/bcl2fastq/bcl2fastq-1.8.4/lib/bcl2fastq-1.8.4/perl/Casava/Alignment.pm line 61.
Compilation failed in require at ./configureBclToFastq.pl line 250.
BEGIN failed--compilation aborted at ./configureBclToFastq.pl line 250.
My perl version is:

Code:
$ perl -v

This is perl 5, version 18, subversion 2 (v5.18.2) built for x86_64-linux-thread-multi
I found this : http://seqanswers.com/forums/showpos...6&postcount=29

but I do not have the root privileges, so any ideas to make it work?
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Old 12-18-2014, 01:30 PM   #19
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@emixaM you do not need root privileges to make that perlbrew hack work.
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Old 12-18-2014, 01:32 PM   #20
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BTW: Is the bgzip2 program in your PATH?
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