bcl2fastq2 install issue

[garchon]

Hi,

I am trying to install the bcl2fastq2 soft with no success on linux debian.
I believe I followed the steps given by the Illumina notice.

From the output below, I understand it can't find or use the sys/stat.h.
But the file is definitely there:
hjg@aurigny:/tmp/bcl2fastq2-v2.15.0.4-build$ locate sys/stat.h
/usr/include/x86_64-linux-gnu/sys/stat.h

In anticipation, thanks very much for your help.

Here is the output of the configure command:

hjg@aurigny:/tmp/bcl2fastq2-v2.15.0.4-build$ sudo ${SOURCE}/src/configure --prefix=${INSTALL_DIR}

cmake version "2.8.9" is already installed at /tmp/bcl2fastq2-v2.15.0.4-build/bootstrap_cmake/bin/cmake
nothing to be done
Using installed /tmp/bcl2fastq2-v2.15.0.4-build/bootstrap_cmake/bin/cmake
-- The C compiler identification is GNU 4.7.2
-- The CXX compiler identification is GNU 4.7.2
-- 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/g++
-- Check for working CXX compiler: /usr/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- install prefix: /usr/local/bin/bcl2fastq2-v2.15.0.4
-- install exec prefix: .
-- install bin dir: ./bin
-- install lib dir: ./lib/bcl2fastq-2.15.0.4
-- install libexec dir: ./libexec/bcl2fastq-2.15.0.4
-- install include dir: include/bcl2fastq-2.15.0.4
-- install data dir: share/bcl2fastq-2.15.0.4
-- install doc dir: doc/bcl2fastq-2.15.0.4
-- install man dir: man
-- Could NOT find Boost
-- Boost 1.54.0 not found. Boost will be built from the distribution...
Decompressing /tmp/bcl2fastq/src/../redist/boost_1_54_0.tar.bz2
Building Boost.Build engine with toolset gcc... tools/build/v2/engine/bin.linuxx86_64/b2
Unicode/ICU support for Boost.Regex?... not found.
Backing up existing Boost.Build configuration in project-config.jam.2
Generating Boost.Build configuration in project-config.jam...

Bootstrapping is done. To build, run:

./b2

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

- Command line help:
./b2 --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

Performing configuration checks

- zlib : yes (cached)
- has_icu builds : no (cached)

Component configuration:

- atomic : not building
- chrono : building
- context : not building
- coroutine : not building
- date_time : building
- exception : not building
- filesystem : building
- graph : not building
- graph_parallel : not building
- iostreams : building
- locale : not building
- log : not 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
- timer : building
- wave : not building

...patience...
...patience...
...found 22368 targets...
boost-1_54_0 installed successfully
-- Successfuly built boost 1.54.0 from the distribution package...
-- Verifying target directories access
-- 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
-- inttypes.h found as /usr/include/inttypes.h
-- malloc.h found as /usr/include/malloc.h
-- mcheck.h found as /usr/include/mcheck.h
-- memory.h found as /usr/include/memory.h
-- signal.h found as /usr/include/signal.h
-- stdint.h found as 1
-- stdlib.h found as /usr/include/stdlib.h
-- string.h found as /usr/include/string.h
-- strings.h found as /usr/include/strings.h
-- time.h found as /usr/include/time.h
-- unistd.h found as /usr/include/unistd.h
CMake Error at cmake/macros.cmake:84 (message):
Required header sys/stat.h not found.
Call Stack (most recent call first):
cmake/cxxConfigure.cmake:44 (bcl2fastq_find_header_or_die)
cxx/CMakeLists.txt:37 (include)


-- Configuring incomplete, errors occurred!
Couldn't configure the project:
/tmp/bcl2fastq2-v2.15.0.4-build/bootstrap_cmake/bin/cmake -H'/tmp/bcl2fastq/src' -B'/tmp/bcl2fastq2-v2.15.0.4-build' -G'Unix Makefiles' -DBCL2FASTQ_NAME_SHORT:STRING="bcl2fastq" -DBCL2FASTQ_NAME_LONG:STRING="BCL to FASTQ file converter" -DBCL2FASTQ_COPYRIGHT:STRING="Copyright (c) 2007-2014 Illumina, Inc." -DBCL2FASTQ_VERSION_MAJOR:STRING="2" -DBCL2FASTQ_VERSION_MINOR:STRING="15" -DBCL2FASTQ_VERSION_PATCH:STRING="0" -DBCL2FASTQ_VERSION_BUILD:STRING="4" -DBCL2FASTQ_VERSION:STRING="2.15.0.4" -DBCL2FASTQ_SOURCE_DIR:STRING="/tmp/bcl2fastq/src" -DBCL2FASTQ_PREFIX:PATH="/usr/local/bin/bcl2fastq2-v2.15.0.4/" -DBCL2FASTQ_EXEC_PREFIX:PATH="" -DCMAKE_INSTALL_PREFIX:PATH="/usr/local/bin/bcl2fastq2-v2.15.0.4/" -DBCL2FASTQ_BINDIR:PATH="" -DBCL2FASTQ_LIBDIR:PATH="" -DBCL2FASTQ_LIBEXECDIR:PATH="" -DBCL2FASTQ_INCLUDEDIR:PATH="" -DBCL2FASTQ_DATADIR:PATH="" -DBCL2FASTQ_DOCDIR:PATH="" -DBCL2FASTQ_MANDIR:PATH="" -DCMAKE_BUILD_TYPE:STRING="RelWithDebInfo" -DCMAKE_PARALLEL:STRING="1"
Moving CMakeCache.txt to CMakeCache.txt.removed

[sarvidsson]

Did you try to install the RPMs with alien instead of compiling from source? For bcl2fastq 1.8.4 this works on Ubuntu (an older Perl interpreter is needed as well).

[garchon]

Thanks for the suggestion.
I tried it.
I downloaded the package from Basespace.
However alien fails:

hjg@aurigny:~$ sudo alien -k bcl2fastq2-v2.15.0.4-linux-x86_64.rpm
Package build failed. Here's the log:
dh_testdir
dh_testdir
dh_testroot
dh_prep
dh_installdirs
dh_installdocs
dh_installchangelogs
parsechangelog/debian: avertissement: debian/changelog(l1): la version « v2.15.0.4-1*» n'est pas valable*: le numéro de version ne commence par par un chiffre
LINE: bcl2fastq2 (v2.15.0.4-1) experimental; urgency=low
find . -maxdepth 1 -mindepth 1 -not -name debian -print0 | \
xargs -0 -r -i cp -a {} debian/bcl2fastq2
dh_compress
dh_makeshlibs
dh_installdeb
dh_shlibdeps
dh_gencontrol
parsechangelog/debian: avertissement: debian/changelog(l1): la version « v2.15.0.4-1*» n'est pas valable*: le numéro de version ne commence par par un chiffre
LINE: bcl2fastq2 (v2.15.0.4-1) experimental; urgency=low
dpkg-gencontrol: avertissement: champ Depends du paquet bcl2fastq2*: variable de substitution inconnue ${shlibsepends}
dh_md5sums
dh_builddeb
dpkg-deb*: erreur*:*analyse du fichier 'debian/bcl2fastq2/DEBIAN/control' vers la ligne 2 paquet 'bcl2fastq2'*:
erreur dans la chaîne Version «*v2.15.0.4-1*»: le numéro de version ne commence pas par un chiffre
dh_builddeb: dpkg-deb --build debian/bcl2fastq2 .. returned exit code 2
make: *** [binary-arch] Erreur 1

Something I would be doing wrong?

[sarvidsson]

Weird - I just tried to alien the same RPM on my Ubuntu 14.04 without any problems.

Did you try to simply remove the offending "v" from "v2.15.0.4-1"? Otherwise you can extract the files from the RPM with

rpm2cpio bcl2fastq2-v2.15.0.4-linux-x86_64.rpm | cpio -dium

[sarvidsson]

Forgot to say that you'll still have to find out the dependencies, however - I guess at least boost, xsltproc and libxml2.

[GenoMax]

@garchon: From your original message.

You could try to make a soft-link for stat.h in /usr/local/include and see if that gets you past the original error.

$ sudo ln -s /usr/include/x86_64-linux-gnu/sys/stat.h /usr/include/sys/stat.h

[garchon]

Sorry for my late feedback.
Many thanks for your very helpful suggestions.

To "sarvidsson":
Removing the offending "v" did not work but "rpm2cpio bcl2fastq2-v2.15.0.4-linux-x86_64.rpm | cpio -dium" did the trick and generated a bcl2fastq executable. There are some differences though between the output of this local bcl2fastq and that of the basespace app. E.g. the header line of the reads end with the index sequences of the sample instead of the sample number. I contacted the illumina tech support to look into this and also about the default settings.

To "Genomax":
Making the soft link worked for stat.h and the configure command was completed fine.
So, thanks.
However, it's the linking that now bugs:

$sudo make
..........
Linking CXX executable bcl2fastq
CMakeFiles/bcl2fastq.dir/bcl2fastq.cpp.o: In function `boost::filesystem:: operator/(boost::filesystem:: path const&, boost::filesystem:: path const&)':
/usr/local/include/boost/filesystem/path.hpp:648: undefined reference to `boost::filesystem:: path:: operator/=(boost::filesystem:: path const&)'
............

The /usr/local/include/boost version is 1.49, installed as a debian package.
The v1.54 recommended by Illumina and installed during the build of bcl2fastq is found at /usr/local/lib/boost_1.54.0/
The BOOST_ROOT was undefined. So I set it to /usr/local/lib/boost_1.54.0/ but it still does not work.

Would you have more helpful ideas?

[GenoMax]

Can you edit your post and enclose the error message above in [QUOTE] [/ QUOTE] (remove the space between / QUOTE when using) tags. It is hard to read otherwise.

What you are seeing is expected behavior of the standalone bcl2fastq. It is actually a useful feature for us.

[sklages]

Sorry for my late feedback.
The /usr/local/include/boost version is 1.49, installed as a debian package.
The v1.54 recommended by Illumina and installed during the build of bcl2fastq is found at /usr/local/lib/boost_1.54.0/
The BOOST_ROOT was undefined. So I set it to /usr/local/lib/boost_1.54.0/ but it still does work.

Would you have more helpful ideas?

Try to additionally set (or wherever lib/include are located):

export BOOST_LIBRARYDIR=$BOOST_ROOT/lib
export BOOST_INCLUDEDIR=$BOOST_ROOT/include

Then configure and rebuild. At least this helped me in an older version of bcl2fastq ..

Where the errors you got with BOOST_ROOT set the same or just similar?

[yifangt]

bcl2fastq installation failed

Hello,
I met the same problem when installing bcl2fastq-v2.17.1.14 from source.
Tried suggestions from this post, none worked.
It seems related to boost library as it tried to install boost_1_54_0 with the package. See the attached log.
I am using GNU/Linux 3.13.0-24-generic x86_64 Mint 17 Qiana
Any suggestions?

Thanks!

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

I just found out the solution by simply under root. As reference to those who hit the same wall, I freshly made subfold under bcl2fastq after unzip the tarball.

mkdir build && cd build
sudo ../src/configre --prefix=/path/where/to/install
sudo make && make install

bcl2fastq automatically handled the boost_1_54_0 installation even I have more updated version. Let it go ahead and it worked for me!

[jstjohn]

As an alternative to the symlink idea, you could just modify your environment. I had to edit/recompress boost 1.54.0 (b/c I am running gcc-4.8) as described here: https://svn.boost.org/trac/boost/ticket/7979. So yeah, I was able to install this to a local prefix w/out root access. Bonus

# needed by boost install
export CPLUS_INCLUDE_PATH=/usr/include/x86_64-linux-gnu:$CPLUS_INCLUDE_PATH

#needed to modify/recompress boost 1.54 in ../redist
# applied the change noted here: https://svn.boost.org/trac/boost/ticket/7979
$SOURCE/src/configure --prefix=${INSTALL_DIR} --parallel=20 --static --build-type Release
make -j 20
make -j 20 install

[biocyberman]

@jstjohn 's answer helped me to install bcl2fastq on Ubuntu 14.04. I also removed linuxbrew which interfered with compilation.