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Old 04-28-2015, 05:55 AM   #1
jov14
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Default problems configuring installation of Bcl2fastq

Hi,
I want to install Bcl2fastq on my system running Ubuntu 14.04.2 LTS. I have admin rights.

However the configure step always aborts with an error.

After running configure I first ran into the typical Error messages of "No support for gzip compression" and "No support for bzip2 compression", so i followed early recommendations here and here, and copied "libz.so", "libpthread*" and "libbz2.so" from /usr/lib/x86_64-linux-gnu/ to /usr/lib.

after that, running "configure" produced this new error message:
Code:
CMake Error at cmake/cxxConfigure.cmake:95 (message):
  libxml2 was not found
As this problem has not been discussed earlier, I tried to use the same approach by copying the libxml2-associated files to /user/lib using the following command:
Code:
sudo cp /usr/lib/x86_64-linux-gnu/libxml2* /usr/local/lib
As this did not help I followed the setup instruction at the end of this thread and this very helpful setup-script to ensure that all dependancies are met.

However I still get the same error message:
Code:
-- Could NOT find LibXml2 (missing:  LIBXML2_LIBRARIES LIBXML2_INCLUDE_DIR) 
CMake Error at cmake/cxxConfigure.cmake:95 (message):
  libxml2 was not found
Call Stack (most recent call first):
  c++/CMakeLists.txt:33 (include)


-- Configuring incomplete, errors occurred!
Couldn't configure the project:

/tmp/bcl2fastq-build/bootstrap/bin/cmake -H"/tmp/bcl2fastq/src" -B"/tmp/bcl2fastq-build" -G"Unix Makefiles"  -DCASAVA_PREFIX:PATH=/usr/local/tools/bcl2fastq-1.8.4 -DCASAVA_EXEC_PREFIX:PATH= -DCMAKE_INSTALL_PREFIX:PATH=/usr/local/tools/bcl2fastq-1.8.4 -DCASAVA_BINDIR:PATH= -DCASAVA_LIBDIR:PATH= -DCASAVA_LIBEXECDIR:PATH= -DCASAVA_INCLUDEDIR:PATH= -DCASAVA_DATADIR:PATH= -DCASAVA_DOCDIR:PATH= -DCASAVA_MANDIR:PATH= -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo

Moving CMakeCache.txt to CMakeCache.txt.removed
Any suggestions?
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Old 04-28-2015, 06:05 AM   #2
GenoMax
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Start with

Code:
$ sudo apt-get install libxml2 libxml2-dev
see if that fixes the error.
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Old 04-28-2015, 06:44 AM   #3
jov14
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Thanks a lot!
I was sure I had libxml2 installed, but i seem to have been mistaken...
Configure now completed without errors. However, now I run into the following errors during "make" at 51%
Code:
[ 51%] Building CXX object c++/lib/io/CMakeFiles/casava_io.dir/PtreeXml.cpp.o
/tmp/bcl2fastq/src/c++/lib/io/PtreeXml.cpp: In function std::ostream& casava::io::operator<<(std::ostream&, const ptree&):
/tmp/bcl2fastq/src/c++/lib/io/PtreeXml.cpp:123:123: error: no matching function for call to xml_writer_make_settings(char, int)
         boost::property_tree::write_xml(os, treeWithIndexAttributes, boost::property_tree::xml_writer_make_settings(' ', 2));
The final error message is:
Code:
make[2]: *** [c++/lib/io/CMakeFiles/casava_io.dir/PtreeXml.cpp.o] Error 1
make[1]: *** [c++/lib/io/CMakeFiles/casava_io.dir/all] Error 2
make: *** [all] Error 2
boost is definitively installed. Do you have suggestions for this also?
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Old 04-28-2015, 06:54 AM   #4
fanli
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Might be an issue with your Boost version. From a different topic, but similar error:
https://github.com/mapnik/mapnik/issues/2365

I was able to install successfuly with Boost 1.55
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Old 04-28-2015, 07:10 AM   #5
jov14
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I have boost version 1.54 installed, which seems to be the newest version of boost in the official Ubuntu repositories.
So I guess that means I should download the most current version of boost directly and compile it manually?
I'll try.
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Old 04-28-2015, 07:11 AM   #6
GenoMax
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Illumina software is picky about version of boost libraries. A local copy here is using boost v.1.44 (which the software built itself).
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Old 04-28-2015, 08:53 AM   #7
jov14
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Hi, everyone.
while trying to figure out how to install which boost library, I simultaneously tried the alternative approach of installing via the Illumina-supplied rpm-package using the instructions here

This now works fine, once expat-2.1.0 and xml-parser-2.41 were installed.

So right now, I am abandoning trying to compile bcl2fastq from source and just work with the successfully installed rpm-package version.

Thanks everyone!
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Old 01-05-2018, 02:08 PM   #8
liorgalanti
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This is for the latest bcl2fastq version 2.20.0 but it seems to be a similar error.

http://backwardincompatible.com/post...on-ubuntu-with
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