CASAVA 1.7 Install Help

[aligenie]

Hi everyone,

I've been trying to install CASAVA 1.7 on Ubuntu 11 and I have an issue during configuration

root@ali-iMac:/usr/local/CASAVA_v1.7.0/CASAVA_v1.7.0-build# /usr/local/CASAVA_v1.7.0/src/configure
cmake version "cmake version 2.8.0" is already installed at /usr/local/CASAVA_v1.7.0/CASAVA_v1.7.0-build/bootstrap/bin/cmake
nothing to be done
Using installed /usr/local/CASAVA_v1.7.0/CASAVA_v1.7.0-build/bootstrap/bin/cmake
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- 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/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- install prefix: /usr/local
-- install exec prefix: .
-- install bin dir: ./bin
-- install lib dir: ./lib/CASAVA-1.7.0
-- install libexec dir: ./libexec/CASAVA-1.7.0
-- install include dir: include/CASAVA-1.7.0
-- install data dir: share/CASAVA-1.7.0
-- install doc dir: doc/CASAVA-1.7.0
-- install man dir: man
-- Verifying target directories access
-- Creating external tools in subdirectory opt
-- Could NOT find Boost
-- Boost 1.41.0 not found. Boost will be built from the distribution...
Decompressing /usr/local/CASAVA_v1.7.0/src/../redist/boost_1_41_0.tar.gz
Building Boost.Jam with toolset gcc... tools/jam/src/bin.linuxx86_64/bjam
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:

./bjam

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

- Command line help:
./bjam --help

- Getting started guide:
http://www.boost.org/more/getting_st...-variants.html

- Boost.Build documentation:
http://www.boost.org/boost-build2/doc/html/index.html

warning: Building Boost.Regex with the optional Unicode/ICU support disabled.
note: Please refer to the Boost.Regex documentation for more information
note: this is a strictly optional feature.
...patience...
...patience...
...found 16182 targets...
...updating 4 targets...
gcc.compile.c++ bin.v2/libs/iostreams/build/gcc-4.5.2/release/link-static/threading-multi/bzip2.o
gcc.archive bin.v2/libs/iostreams/build/gcc-4.5.2/release/link-static/threading-multi/libboost_iostreams.a
common.copy /usr/local/CASAVA_v1.7.0/CASAVA_v1.7.0-build/opt/bootstrap/lib/libboost_iostreams.a
...updated 4 targets...
boost-1_41_0 installed successfully
-- Successfuly built boost 1.41.0 from the distribution package...
-- Installing Post-Run Command Framework
-- 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
CMake Error at cmake/cxxConfigure.cmake:71 (message):
No support for gzip compression
Call Stack (most recent call first):
c++/CMakeLists.txt:30 (include)


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

/usr/local/CASAVA_v1.7.0/CASAVA_v1.7.0-build/bootstrap/bin/cmake -H"/usr/local/CASAVA_v1.7.0/src" -B"/usr/local/CASAVA_v1.7.0/CASAVA_v1.7.0-build" -G"Unix Makefiles" -DCASAVA_PREFIX:PATH= -DCASAVA_EXEC_PREFIX:PATH= -DCMAKE_INSTALL_PREFIX:PATH= -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


Can anyone tell what is going wrong?

Thanks in advance!

Ali

[sklages]

Originally Posted by aligenie

Hi everyone,

I've been trying to install CASAVA 1.7 on Ubuntu 11 and I have an issue during configuration

[...]
CMake Error at cmake/cxxConfigure.cmake:71 (message):
No support for gzip compression
[...]

Can anyone tell what is going wrong?

Have a look if libz header files are installed; check for dev package in synaptic.

libz (>=1.2.3) <http://www.zlib.net> is a requirement.

hth,
Sven

[dweebis]

I have the same error, and am certain that I've installed the zlib's. Have you found any other way to resolve this issue?

Dweeb

[sklages]

Originally Posted by dweebis

I have the same error, and am certain that I've installed the zlib's. Have you found any other way to resolve this issue?

Dweeb

Sure you have installed the dev package (header files)? AFAIR

libzzip-0-13 - library providing read access on ZIP-archives - library
libzzip-dev - library providing read access on ZIP-archives - development

Keep in mind that CASAVA 1.8 is out ...

hth, Sven

[dweebis]

I did not have those installed....but I still have the same problem. Ergh.

Thanks for trying -

Dweeb

[dweebis]

Oh - does 1.8 compile where 1.7 doesn't. I'll check compatibility...

[dweebis]

Here's the error this time:

-- Looking for erfc - found
CMake Error at cmake/cxxConfigure.cmake:74 (message):
  No support for gzip compression
Call Stack (most recent call first):
  c++/CMakeLists.txt:33 (include)


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

/media/bigjoe/mpufall/software/CASAVA-1.8.1-build/bootstrap/bin/cmake -H"/media/bigjoe/mpufall/software/CASAVA_v1.8.1/src" -B"/media/bigjoe/mpufall/software/CASAVA-1.8.1-build" -G"Unix Makefiles"  -DCASAVA_PREFIX:PATH=/media/bigjoe/mpufall/software/CASAVA-1.8.1 -DCASAVA_EXEC_PREFIX:PATH= -DCMAKE_INSTALL_PREFIX:PATH=/media/bigjoe/mpufall/software/CASAVA-1.8.1 -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

I'm tracking this down with Illumina...something is funny here...

Dweeb

[sklages]

what system you are running? Distribution 64bit?

If you have installed zlib development files you can point configure to that location (assuming it is a "non standard" location where zlib headers are installed),

export CPPFLAGS="-I/path/to/headers"
./configure --verbose --prefix=/where/to/put/casava

should work (in theory) .. but we all know that casava is sometimes very special ;-)
The verbose option should give you a more detailed hint.

hth, Sven

[dweebis]

Hi Sven -

OK - after some effort, I was able to get CASAVA-1.8.1 installed, but not 1.7.0 (which I need at this point as part of a methylation pipeline). Everything was installed, but some things were in this new /usr/linb64/x86_64-linux.gnu instead of just /usr/lib64. As I'm not the slickest guy in the world, I just copied the relevant libraries into /usr/lib64:

sudo cp /usr/lib64/x86_64-linux-gnu/zlib.so ..
sudo cp /usr/lib64/x86_64-linux-gnu/libpthread* ..

I also had to end up installing doxygen:
sudo apt-get install doxygen

Then everything went fine for CASAVA-1.8.1. Not so for 1.7.0, which completed configure, but failed during make. I may work on this a bit more, but actually to cope I just set up a machine with Lucid 10.04 LTS, and everything installed (and works) beautifully.

Cheers -

Dweebis

[kalyankpy]

Hi,

I have faced the same problem while configuring the CASAVA1.8.2 on Ubuntu 11.10 (64bit). After going through this thread I followed the same strategy to copy the libz.so and libpthread* to /usr/lib folder. This helped me configure casava successfully.

Commands I have used

$ sudo cp /usr/lib/x86_64-linux-gnu/libz.so /usr/lib
$ sudo cp /usr/lib/x86_64-linux-gnu/libpthread* /usr/lib

I am writing this just to mention that the same strategy works for CASAVA 1.8.2 on ubuntu 11.10.

Kalyan

Originally Posted by aligenie

Hi everyone,

I've been trying to install CASAVA 1.7 on Ubuntu 11 and I have an issue during configuration

root@ali-iMac:/usr/local/CASAVA_v1.7.0/CASAVA_v1.7.0-build# /usr/local/CASAVA_v1.7.0/src/configure
cmake version "cmake version 2.8.0" is already installed at /usr/local/CASAVA_v1.7.0/CASAVA_v1.7.0-build/bootstrap/bin/cmake
nothing to be done
Using installed /usr/local/CASAVA_v1.7.0/CASAVA_v1.7.0-build/bootstrap/bin/cmake
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- 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/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- install prefix: /usr/local
-- install exec prefix: .
-- install bin dir: ./bin
-- install lib dir: ./lib/CASAVA-1.7.0
-- install libexec dir: ./libexec/CASAVA-1.7.0
-- install include dir: include/CASAVA-1.7.0
-- install data dir: share/CASAVA-1.7.0
-- install doc dir: doc/CASAVA-1.7.0
-- install man dir: man
-- Verifying target directories access
-- Creating external tools in subdirectory opt
-- Could NOT find Boost
-- Boost 1.41.0 not found. Boost will be built from the distribution...
Decompressing /usr/local/CASAVA_v1.7.0/src/../redist/boost_1_41_0.tar.gz
Building Boost.Jam with toolset gcc... tools/jam/src/bin.linuxx86_64/bjam
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:

./bjam

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

- Command line help:
./bjam --help

- Getting started guide:
http://www.boost.org/more/getting_st...-variants.html

- Boost.Build documentation:
http://www.boost.org/boost-build2/doc/html/index.html

warning: Building Boost.Regex with the optional Unicode/ICU support disabled.
note: Please refer to the Boost.Regex documentation for more information
note: this is a strictly optional feature.
...patience...
...patience...
...found 16182 targets...
...updating 4 targets...
gcc.compile.c++ bin.v2/libs/iostreams/build/gcc-4.5.2/release/link-static/threading-multi/bzip2.o
gcc.archive bin.v2/libs/iostreams/build/gcc-4.5.2/release/link-static/threading-multi/libboost_iostreams.a
common.copy /usr/local/CASAVA_v1.7.0/CASAVA_v1.7.0-build/opt/bootstrap/lib/libboost_iostreams.a
...updated 4 targets...
boost-1_41_0 installed successfully
-- Successfuly built boost 1.41.0 from the distribution package...
-- Installing Post-Run Command Framework
-- 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
CMake Error at cmake/cxxConfigure.cmake:71 (message):
No support for gzip compression
Call Stack (most recent call first):
c++/CMakeLists.txt:30 (include)


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

/usr/local/CASAVA_v1.7.0/CASAVA_v1.7.0-build/bootstrap/bin/cmake -H"/usr/local/CASAVA_v1.7.0/src" -B"/usr/local/CASAVA_v1.7.0/CASAVA_v1.7.0-build" -G"Unix Makefiles" -DCASAVA_PREFIX:PATH= -DCASAVA_EXEC_PREFIX:PATH= -DCMAKE_INSTALL_PREFIX:PATH= -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


Can anyone tell what is going wrong?

Thanks in advance!

Ali

[ObOlli]

Hi, an old thread I know, but some fresh experience.

We still run Ubuntu 10.04.x in our servers, hence in all our systems. One becomes conservative with experience, and I'd never want to run a non-LTS in an actual prodution environment.

First, I would suggest making a symlink like I did instead of copying the libraries, so as not to leave dangling libraries behind (these can lead to hard-to-debug problems in later maintenance) :

$ ln -s /usr/lib/x86_64-linux-gnu/libz.so /usr/lib
$ ln -s /usr/lib/x86_64-linux-gnu/libpthread* /usr/lib

Once that is done, I succeeded even compiling 1.8.2 as static. Of course, quite a few .deb packages needed to be added to our barebones installation (in a real server you never want to install everything between heaven and earth,) and I'd have to install a new workstation to see precisely what. Two that stuck in my mind are ImageMagick and GraphViz, which appeared to be necessary for documentation only. Blecch.

Here's the commands I used:

$ ionice -c3 ../CASAVA_v1.8.2/src/configure --prefix=/usr/local/biotools/CASAVA_v1.8.2 --with-cmake=`which cmake` --static
$ ionice -c3 make -j2
$ make install

The actual configure and compilation, apart from thrashing my hard disk peformance for which reason ionice, did crash in internal error. I just tried again.

I prefer useing the system-installed cmake since (ie. from .deb,) although it didn't solve the Redhat-specific idiocies.

Yours, ObOlli

Originally Posted by kalyankpy

Hi,

I have faced the same problem while configuring the CASAVA1.8.2 on Ubuntu 11.10 (64bit). After going through this thread I followed the same strategy to copy the libz.so and libpthread* to /usr/lib folder. This helped me configure casava successfully.

Commands I have used

$ sudo cp /usr/lib/x86_64-linux-gnu/libz.so /usr/lib
$ sudo cp /usr/lib/x86_64-linux-gnu/libpthread* /usr/lib

I am writing this just to mention that the same strategy works for CASAVA 1.8.2 on ubuntu 11.10.

Kalyan

[slees]

Hi,

I was trying to install the CASAVA Bcl2Fastq 1.8.3 package on my Ubuntu Server 12.04LTS. First, I encountered the same "No support for gzip compression" discussed in this thread, and the solution here solved this problem However, now it prompts: "No support for bzip2 compression".
I am wondering if there is any way to solve this?

Here is the detailed install log:

administrator@Epizyme2:/tmp/bcl2fastq-1.8.3-build$ sudo ${SOURCE}/src/configure --prefix=${INSTALL} --verbose
[sudo] password for administrator: 
cmake version "cmake version 2.8.4" is already installed at /tmp/bcl2fastq-1.8.3-build/bootstrap/bin/cmake
nothing to be done
Using installed /tmp/bcl2fastq-1.8.3-build/bootstrap/bin/cmake
Source  directory: /tmp/bcl2fastq-1.8.3/src
Prefix  directory: /usr/local/bcl2fastq-1.8.3
Exec    directory: 
Binary  directory: 
Lib     directory: 
Libexec directory: 
Include directory: 
Data    directory: 
Doc     directory: 
Man     directory: 
Build   directory: /tmp/bcl2fastq-1.8.3-build
Cmake  executable: /tmp/bcl2fastq-1.8.3-build/bootstrap/bin/cmake

Running on: Linux Epizyme2 3.2.0-29-generic #46-Ubuntu SMP Fri Jul 27 17:03:23 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
Configuring the build directory with:
    /tmp/bcl2fastq-1.8.3-build/bootstrap/bin/cmake -H"/tmp/bcl2fastq-1.8.3/src" -B"/tmp/bcl2fastq-1.8.3-build" -G"Unix Makefiles" -DCASAVA_PREFIX:PATH=/usr/local/bcl2fastq-1.8.3 -DCASAVA_EXEC_PREFIX:PATH= -DCMAKE_INSTALL_PREFIX:PATH=/usr/local/bcl2fastq-1.8.3 -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 -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DBoost_DEBUG:BOOL=ON

-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- 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/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- install      prefix: /usr/local/bcl2fastq-1.8.3
-- install exec prefix: .
-- install     bin dir: ./bin
-- install     lib dir: ./lib/bcl2fastq-1.8.3
-- install libexec dir: ./libexec/bcl2fastq-1.8.3
-- install include dir: include/bcl2fastq-1.8.3
-- install    data dir: share/bcl2fastq-1.8.3
-- install     doc dir: doc/bcl2fastq-1.8.3
-- install     man dir: man
-- Verifying target directories access
-- Creating external tools in subdirectory opt
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:461 ] Boost not in cache
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:464 ] _boost_TEST_VERSIONS = 1.46.0;1.46;1.45.0;1.45;1.44.0;1.44
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:466 ] Boost_USE_MULTITHREADED = TRUE
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:468 ] Boost_USE_STATIC_LIBS = 
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:470 ] Boost_USE_STATIC_RUNTIME = 
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:472 ] Boost_ADDITIONAL_VERSIONS = 
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:474 ] Boost_NO_SYSTEM_PATHS = 
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:537 ] Declared as CMake or Environmental Variables:
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:539 ]   BOOST_ROOT = 
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:541 ]   BOOST_INCLUDEDIR = 
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:543 ]   BOOST_LIBRARYDIR = 
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:545 ] _boost_TEST_VERSIONS = 1.46.0;1.46;1.45.0;1.45;1.44.0;1.44
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:598 ] Include debugging info:
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:600 ]   _boost_INCLUDE_SEARCH_DIRS = C:/boost/include;C:/boost;/boost/include;/boost;/sw/local/include
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:602 ]   _boost_PATH_SUFFIXES = boost-1_46_0;boost_1_46_0;boost-1_46;boost_1_46;boost-1_45_0;boost_1_45_0;boost-1_45;boost_1_45;boost-1_44_0;boost_1_44_0;boost-1_44;boost_1_44
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:737 ] guessed _boost_COMPILER = -gcc
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:747 ] _boost_MULTITHREADED = -mt
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:790 ] _boost_RELEASE_ABI_TAG = -
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:792 ] _boost_DEBUG_ABI_TAG = -d
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:835 ] _boost_LIBRARY_SEARCH_DIRS = Boost_INCLUDE_DIR-NOTFOUND/lib;Boost_INCLUDE_DIR-NOTFOUND/../lib;Boost_INCLUDE_DIR-NOTFOUND/stage/lib;C:/boost/lib;C:/boost;/boost/boost___/lib;/boost/boost__/lib;/boost/lib;/boost;/sw/local/lib
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for DATE_TIME_LIBRARY_RELEASE: boost_date_time-gcc-mt-;boost_date_time-gcc-mt;boost_date_time-mt-;boost_date_time-mt;boost_date_time
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for DATE_TIME_LIBRARY_DEBUG: boost_date_time-gcc-mt-d-;boost_date_time-gcc-mt-d;boost_date_time-mt-d-;boost_date_time-mt-d;boost_date_time-mt;boost_date_time
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for FILESYSTEM_LIBRARY_RELEASE: boost_filesystem-gcc-mt-;boost_filesystem-gcc-mt;boost_filesystem-mt-;boost_filesystem-mt;boost_filesystem
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for FILESYSTEM_LIBRARY_DEBUG: boost_filesystem-gcc-mt-d-;boost_filesystem-gcc-mt-d;boost_filesystem-mt-d-;boost_filesystem-mt-d;boost_filesystem-mt;boost_filesystem
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for IOSTREAMS_LIBRARY_RELEASE: boost_iostreams-gcc-mt-;boost_iostreams-gcc-mt;boost_iostreams-mt-;boost_iostreams-mt;boost_iostreams
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for IOSTREAMS_LIBRARY_DEBUG: boost_iostreams-gcc-mt-d-;boost_iostreams-gcc-mt-d;boost_iostreams-mt-d-;boost_iostreams-mt-d;boost_iostreams-mt;boost_iostreams
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for PROGRAM_OPTIONS_LIBRARY_RELEASE: boost_program_options-gcc-mt-;boost_program_options-gcc-mt;boost_program_options-mt-;boost_program_options-mt;boost_program_options
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for PROGRAM_OPTIONS_LIBRARY_DEBUG: boost_program_options-gcc-mt-d-;boost_program_options-gcc-mt-d;boost_program_options-mt-d-;boost_program_options-mt-d;boost_program_options-mt;boost_program_options
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for REGEX_LIBRARY_RELEASE: boost_regex-gcc-mt-;boost_regex-gcc-mt;boost_regex-mt-;boost_regex-mt;boost_regex
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for REGEX_LIBRARY_DEBUG: boost_regex-gcc-mt-d-;boost_regex-gcc-mt-d;boost_regex-mt-d-;boost_regex-mt-d;boost_regex-mt;boost_regex
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for SERIALIZATION_LIBRARY_RELEASE: boost_serialization-gcc-mt-;boost_serialization-gcc-mt;boost_serialization-mt-;boost_serialization-mt;boost_serialization
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for SERIALIZATION_LIBRARY_DEBUG: boost_serialization-gcc-mt-d-;boost_serialization-gcc-mt-d;boost_serialization-mt-d-;boost_serialization-mt-d;boost_serialization-mt;boost_serialization
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for SYSTEM_LIBRARY_RELEASE: boost_system-gcc-mt-;boost_system-gcc-mt;boost_system-mt-;boost_system-mt;boost_system
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for SYSTEM_LIBRARY_DEBUG: boost_system-gcc-mt-d-;boost_system-gcc-mt-d;boost_system-mt-d-;boost_system-mt-d;boost_system-mt;boost_system
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for THREAD_LIBRARY_RELEASE: boost_thread-gcc-mt-;boost_thread-gcc-mt;boost_thread-mt-;boost_thread-mt;boost_thread
-- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for THREAD_LIBRARY_DEBUG: boost_thread-gcc-mt-d-;boost_thread-gcc-mt-d;boost_thread-mt-d-;boost_thread-mt-d;boost_thread-mt;boost_thread
-- Could NOT find Boost
Unable to find the Boost header files. Please set BOOST_ROOT to the root directory containing Boost or BOOST_INCLUDEDIR to the directory containing Boost's headers.
-- Boost 1.44.0 not found. Boost will be built from the distribution...
Decompressing /tmp/bcl2fastq-1.8.3/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.
Backing up existing Boost.Build configuration in project-config.jam.5
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

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...
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
-- Found ZLIB  header: /usr/include/zlib.h
-- Found ZLIB library: /usr/lib/libz.so
-- 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!
Couldn't configure the project:

/tmp/bcl2fastq-1.8.3-build/bootstrap/bin/cmake -H"/tmp/bcl2fastq-1.8.3/src" -B"/tmp/bcl2fastq-1.8.3-build" -G"Unix Makefiles"  -DCASAVA_PREFIX:PATH=/usr/local/bcl2fastq-1.8.3 -DCASAVA_EXEC_PREFIX:PATH= -DCMAKE_INSTALL_PREFIX:PATH=/usr/local/bcl2fastq-1.8.3 -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 -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DBoost_DEBUG:BOOL=ON

Moving CMakeCache.txt to CMakeCache.txt.removed

[ersgupta]

@slees... i had the same problem, and this solved it...

sudo cp /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib

[TonyBrooks]

I can configure in without problems, but I get a ton of boost errors when I try to run make

[CODE]/usr/local/include/boost/bind/bind.hpp:1728:1: note:   template argument deduction/substitution failed:
/home/uclg-admin/bcl/bcl2fastq/src/c++/lib/demultiplex/BclDemultiplexer.cpp:65:50: note:   couldn't deduce template parameter ‘M’
                 boost::bind(&fs::path::string, _1));
                                                  ^
make[2]: *** [c++/lib/demultiplex/CMakeFiles/casava_demultiplex.dir/BclDemultiplexer.cpp.o] Error 1
make[1]: *** [c++/lib/demultiplex/CMakeFiles/casava_demultiplex.dir/all] Error 2
make: *** [all] Error 2[/CODE]

Boost was already complied on this machine, but I've tried removing all traces using sudo apt-get purge libboost* but still no joy

[GenoMax]

Tony: Do you need 1.7 for some specific reason? It may be better to go with bcl2fastq (v.1.8.4) otherwise.

[TonyBrooks]

Originally Posted by GenoMax

Tony: Do you need 1.7 for some specific reason? It may be better to go with bcl2fastq (v.1.8.4) otherwise.

Sorry, this is bcl2fastq 1.8.4. Thought it easier to post to the same thread as CASSAVA as bcl2fastq is/was part of CASSAVA

[GenoMax]

Can you try installing the rpm package (http://namhuy.net/1207/how-to-instal...-debian.html)? That may be simpler.

[TonyBrooks]

Originally Posted by GenoMax

Can you try installing the rpm package (http://namhuy.net/1207/how-to-instal...-debian.html)? That may be simpler.

I tried that. I could get the deb created but installing fails with no errors after unpacking.

admin@seq-analysis:~/bcl$ sudo alien bcl2fastq-1.8.4-Linux-x86_64.rpm 
bcl2fastq_1.8.4-2_amd64.deb generated
admin@seq-analysis:~/bcl$ sudo dpkg -i bcl2fastq_1.8.4-2_amd64.deb 
(Reading database ... 273160 files and directories currently installed.)
Preparing to unpack bcl2fastq_1.8.4-2_amd64.deb ...
Unpacking bcl2fastq (1.8.4-2) over (1.8.4-2) ...
Setting up bcl2fastq (1.8.4-2) ...
admin@seq-analysis:~/bcl

I should add that Setting up bcl2fastq lasts about 3 seconds before exiting. configureBclTofastq.pl goes into my path, but returns errors when I try and run it.

configureBclTofastq.pl --input-dir ./140321_M01520_0085_000000000-A7FD0/Data/Intensities/BaseCalls/
"my" variable $value masks earlier declaration in same statement at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 760.
syntax error at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 747, near "$variable qw(ELAND_FASTQ_FILES_PER_PROCESS)"
Global symbol "$variable" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 749.
syntax error at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 751, near "$directory qw(ELAND_GENOME)"
Global symbol "$self" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
Global symbol "$directory" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
Global symbol "$project" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
Global symbol "$sample" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
Global symbol "$lane" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
Global symbol "$barcode" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
Global symbol "$reference" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
syntax error at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 761, near "}"
/usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm has too many errors.
Compilation failed in require at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment.pm line 61.
BEGIN failed--compilation aborted at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment.pm line 61.
Compilation failed in require at /usr/local/bin/configureBclToFastq.pl line 250.
BEGIN failed--compilation aborted at /usr/local/bin/configureBclToFastq.pl line 250.

[GenoMax]

Tony: You need to minimally provide a samplesheet by specifying --samplesheet Samphesheet_file.csv (it needs to be in a specific format). I have an example in this post: http://seqanswers.com/forums/showpos...4&postcount=14

Can you try this?

$ configureBclTofastq.pl --input-dir ./140321_M01520_0085_000000000-A7FD0/Data/Intensities/BaseCalls/ --samplesheet /path_to/samplesheet.csv --fastq-cluster-count 0

--fastq-cluster-count makes a single gz file for a sample. If you do not want that then remove that option.

[TonyBrooks]

Originally Posted by GenoMax

Tony: You need to minimally provide a samplesheet by specifying --samplesheet Samphesheet_file.csv (it needs to be in a specific format). I have an example in this post: http://seqanswers.com/forums/showpos...4&postcount=14

Can you try this?

$ configureBclTofastq.pl --input-dir ./140321_M01520_0085_000000000-A7FD0/Data/Intensities/BaseCalls/ --samplesheet /path_to/samplesheet.csv --fastq-cluster-count 0

--fastq-cluster-count makes a single gz file for a sample. If you do not want that then remove that option.

Same problem
I think I may have found the problem. I'm wondering if the problem is to do with the version of boost installed. I'm going to try and remove and install an older version and see if it works