HELP! CASAVA_v1.7.0 Install error:pthread library not found

[soofree]

Hi everyone,

I've been trying to install CASAVA 1.7 and run into following errors when configuration.

$../CASAVA_v1.7.0/src/configure

cmake version "cmake version 2.8.0" is already installed at /usr/local/bio-soft/CASAVA_v1.7.0-build/bootstrap/bin/cmake
nothing to be done
Using installed /usr/local/bio-soft/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/bio-soft/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.1
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

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...
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
-- Found ZLIB header: /usr/include/zlib.h
-- Found ZLIB library: /usr/lib/libz.so
-- gzip compression supported
-- Found BZIP2 header: /usr/include/bzlib.h
-- Found BZIP2 library: /usr/lib/libbz2.so
-- bzip2 compression supported
-- pthread headers: /usr/include
-- pthread library: PTHREAD_LIBRARY-NOTFOUND
CMake Error at cmake/macros.cmake:87 (message):
pthread library is required to build the CASAVA
Call Stack (most recent call first):
cmake/cxxConfigure.cmake:84 (casava_find_boost)
c++/CMakeLists.txt:30 (include)


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

/usr/local/bio-soft/CASAVA_v1.7.0-build/bootstrap/bin/cmake -H"/usr/local/bio-soft/CASAVA_v1.7.0/src" -B"/usr/local/bio-soft/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

[GenoMax]

Not directly answering your question but is there a specific reason that you are trying to install pipeline v.1.7? Pipeline v.1.8 is out.

[soofree]

Not directly answering your question but is there a specific reason that you are trying to install pipeline v.1.7? Pipeline v.1.8 is out.

I have installed V1.8 , but some related scripts prefer v.1.7. Thank you for your replies.

Regards,

[soofree]

Not directly answering your question but is there a specific reason that you are trying to install pipeline v.1.7? Pipeline v.1.8 is out.

The CASAVA 1.7 output is Illumina 1.3+ FASTQ format, Our script only support that format. However, CASAVA 1.8 gives out Sanger FASTQ files. I want to know if the CASAVA 1.8 FASTQ format supported by SOAP denovo and BWA directly?

[dweebis]

Hi Soofree -

I'm having the same issue - any resolution?

Dweeb

[tgenahmet]

--static

I ran into the same problem when I used --static while running configure. Removed --static and now it is past that step.

[Richard Finney]

Lots of information but the critical lines here are

-- pthread library: PTHREAD_LIBRARY-NOTFOUND
CMake Error at cmake/macros.cmake:87 (message):
pthread library is required to build the CASAVA

You need the pthread library.

[weasteam]

Ho yeah, I am back with solutions:

In linux, try following two lines in termnal:

sudo ln -s /usr/lib/x86_64_linux_gun/lib2.so /usr/lib
sudo ln -s /usr/lib/x86_64_linux_gun/libpth* /usr/lib

[sheenams]

The two link commands worked for me. Just make sure you don't copy and paste as they both say 'gun' instead of 'gnu'