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Similar Threads
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| Thread | Thread Starter | Forum | Replies | Last Post |
| Issues with CASAVA 1.8.1 | Orr Shomroni | Bioinformatics | 19 | 09-13-2015 03:14 PM |
| CASAVA-1.8 install fails | roko-t | Illumina/Solexa | 27 | 06-04-2013 03:59 AM |
| Demultiplexing and CASAVA 1.7 | tonio100680 | Bioinformatics | 14 | 06-16-2011 10:48 PM |
| CASAVA-1.7.0 install fails | sehrrot | Bioinformatics | 2 | 05-24-2011 04:08 AM |
| CASAVA installation | sehrrot | Bioinformatics | 1 | 11-08-2010 04:21 AM |
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Thread Tools |
05-03-2011, 12:02 PM
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#1 |
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Member
Location: San Diego Join Date: Feb 2011
Posts: 13
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CASAVA 1.7 Install Help
Hi everyone,
I've been trying to install CASAVA 1.7 on Ubuntu 11 and I have an issue during configuration [email protected]:/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 |
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05-03-2011, 11:24 PM
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#2 | |
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Senior Member
Location: Berlin, DE Join Date: May 2008
Posts: 620
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Quote:
libz (>=1.2.3) <http://www.zlib.net> is a requirement. hth, Sven |
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09-13-2011, 11:30 AM
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#3 |
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Junior Member
Location: California Join Date: May 2009
Posts: 8
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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 |
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09-13-2011, 11:42 AM
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#4 | |
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Senior Member
Location: Berlin, DE Join Date: May 2008
Posts: 620
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Quote:
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 |
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09-13-2011, 11:59 AM
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#5 |
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Junior Member
Location: California Join Date: May 2009
Posts: 8
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I did not have those installed....but I still have the same problem. Ergh.
Thanks for trying - Dweeb |
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09-13-2011, 12:00 PM
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#6 |
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Junior Member
Location: California Join Date: May 2009
Posts: 8
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Oh - does 1.8 compile where 1.7 doesn't. I'll check compatibility...
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09-13-2011, 06:30 PM
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#7 |
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Junior Member
Location: California Join Date: May 2009
Posts: 8
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Essentially the same error with CASAVA-1.8.1
Here's the error this time:
HTML Code:
-- 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 Dweeb |
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09-13-2011, 10:36 PM
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#8 | |
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Senior Member
Location: Berlin, DE Join Date: May 2008
Posts: 620
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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), Quote:
The verbose option should give you a more detailed hint. hth, Sven |
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09-23-2011, 08:43 AM
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#9 |
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Junior Member
Location: California Join Date: May 2009
Posts: 8
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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 |
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11-19-2011, 08:11 AM
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#10 | |
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PostDoc
Location: Turku, Finland Join Date: Mar 2010
Posts: 20
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Installation problem in CASAVA1.8.2
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 Quote:
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01-27-2012, 02:12 AM
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#11 | |
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Junior Member
Location: Helsinki, Finland Join Date: Jan 2012
Posts: 1
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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 Quote:
__________________
Just an IT specialist and administrator at a smallish lab |
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01-29-2013, 01:34 PM
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#12 |
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Member
Location: NC Join Date: May 2012
Posts: 11
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CASAVA 1.8.3 install error on Ubuntu 12.04LTS: "No support for bzip2 compression"
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: Code:
[email protected]:/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 |
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05-21-2013, 03:48 AM
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#13 |
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Member
Location: India Join Date: Jun 2011
Posts: 26
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@slees... i had the same problem, and this solved it...
sudo cp /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib
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05-01-2014, 04:59 AM
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#14 |
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Senior Member
Location: London Join Date: Jun 2009
Posts: 298
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14.04 LTS boost errors
I can configure in without problems, but I get a ton of boost errors when I try to run make
HTML Code:
[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 |
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05-01-2014, 05:18 AM
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#15 |
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Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 6,780
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Tony: Do you need 1.7 for some specific reason? It may be better to go with bcl2fastq (v.1.8.4) otherwise.
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05-01-2014, 05:31 AM
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#16 | |
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Senior Member
Location: London Join Date: Jun 2009
Posts: 298
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Quote:
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05-01-2014, 06:06 AM
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#17 |
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Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 6,780
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Can you try installing the rpm package (http://namhuy.net/1207/how-to-instal...-debian.html)? That may be simpler.
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05-01-2014, 07:09 AM
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#18 | |
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Senior Member
Location: London Join Date: Jun 2009
Posts: 298
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Quote:
Code:
[email protected]:~/bcl$ sudo alien bcl2fastq-1.8.4-Linux-x86_64.rpm bcl2fastq_1.8.4-2_amd64.deb generated [email protected]:~/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) ... [email protected]:~/bcl Code:
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. Last edited by TonyBrooks; 05-01-2014 at 07:19 AM. |
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05-01-2014, 07:56 AM
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#19 |
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Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 6,780
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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? Code:
$ configureBclTofastq.pl --input-dir ./140321_M01520_0085_000000000-A7FD0/Data/Intensities/BaseCalls/ --samplesheet /path_to/samplesheet.csv --fastq-cluster-count 0 Last edited by GenoMax; 05-01-2014 at 08:00 AM. |
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05-01-2014, 09:07 AM
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#20 | |
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Senior Member
Location: London Join Date: Jun 2009
Posts: 298
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Quote:
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 |
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