CASAVA 1.8.2 Installation problem

[georgeg9]

Hello,

I am trying to install CASAVA on my Gentoo system and I get the following error.

[ 0%] Built target CASAVA_SAMTOOLS
[ 0%] Building illumina_samtools_extensions
bam_cat.c: In function 'bam_cat':
bam_cat.c:122:23: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result]
bam_cat.c:126:32: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result]
bam_cat.c:129:23: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result]
bam_cat.c:142:23: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result]
[ 0%] Built target CASAVA_ILMNSAMTOOLS
[ 0%] Unpacking merge.xslt
[ 1%] Built target CASAVA_MERGE_XSLT
[ 1%] Extracting the Chart director library and tools
[ 1%] Built target CASAVA_CHART_DIRECTOR
[ 1%] Extracting the CodeMin headers and examples
[ 2%] Built target CASAVA_CODE_MIN
[ 2%] Built target CASAVA_OPT
[ 12%] Built target casava_blt_util
[ 19%] Built target casava_blt_common
[ 20%] Built target casava_blt
[ 32%] Built target casava_starling
[ 45%] Built target casava_common
[ 46%] Built target casava_io
[ 50%] Built target casava_alignment
[ 51%] Built target casava_basecalling
[ 51%] Built target casava_assembly
[ 58%] Built target casava_variance
[ 58%] Building CXX object c++/lib/applications/CMakeFiles/casava_applications.dir/AlignContig.cpp.o
/home/george/Downloads/CASAVA_v1.8.2/src/c++/lib/applications/AlignContig.cpp: In member function 'int ca::applications::AlignContig::run()':
/home/george/Downloads/CASAVA_v1.8.2/src/c++/lib/applications/AlignContig.cpp:569:87: error: conversion from 'boost::filesystem3:ath' to non-scalar type 'std::string {aka std::basic_string<char>}' requested
make[2]: *** [c++/lib/applications/CMakeFiles/casava_applications.dir/AlignContig.cpp.o] Error 1
make[1]: *** [c++/lib/applications/CMakeFiles/casava_applications.dir/all] Error 2
make: *** [all] Error 2

[sklages]

hmm, which versions of compiler and boost are you using?

Btw, why 1.8.2? Current version is 1.8.4 (OK, without Eland/SNP caller).

[john789]

I'm getting a very similar error with casava version 1.8.2.

sklages or anyone - Where can I download version 1.8.4? I've searched but can't find it.
georgeg9 - Did you find a different solution?

Thanks
John

[CASAVA_v1.8.2-build]$ export BOOST_ROOT=/usr/local/boost_1_53_0
[CASAVA_v1.8.2-build]$ ../CASAVA_v1.8.2/src/configure 
cmake version "cmake version 2.8.4" is already installed at /home/john/Downloads/cassava/CASAVA_v1.8.2-build/bootstrap/bin/cmake
nothing to be done
Using installed /home/john/Downloads/cassava/CASAVA_v1.8.2-build/bootstrap/bin/cmake
-- install      prefix: /usr/local
-- install exec prefix: .
-- install     bin dir: ./bin
-- install     lib dir: ./lib/CASAVA-1.8.2
-- install libexec dir: ./libexec/CASAVA-1.8.2
-- install include dir: include/CASAVA-1.8.2
-- install    data dir: share/CASAVA-1.8.2
-- install     doc dir: doc/CASAVA-1.8.2
-- install     man dir: man
-- Verifying target directories access
-- Creating external tools in subdirectory opt
-- Found ZLIB  header: /usr/local/include/zlib.h
-- Found ZLIB library: /usr/local/lib/libz.so
-- gzip compression supported
-- Found BZIP2  header: /usr/include/bzlib.h
-- Found BZIP2 library: /usr/lib64/libbz2.so
-- bzip2 compression supported
-- Found PTHREAD  header: /usr/include/pthread.h
-- Found PTHREAD library: /usr/lib64/libpthread.so
-- pthread supported
-- Found X11  header: /usr/include/X11/X.h
-- Found X11 library: /usr/lib64/libX11.so
-- using compiler: gcc version 4.7.2
-- Adding the c++    library subdirectory: blt_util
-- Adding the c++    library subdirectory: blt_common
-- Adding the c++    library subdirectory: blt
-- Adding the c++    library subdirectory: starling
-- Adding the c++    library subdirectory: common
-- Adding the c++    library subdirectory: io
-- Adding the c++    library subdirectory: alignment
-- Adding the c++    library subdirectory: basecalling
-- Adding the c++    library subdirectory: assembly
-- Adding the c++    library subdirectory: variance
-- Adding the c++    library subdirectory: applications
-- Adding the c++    library subdirectory: demultiplex
-- Adding the c++    library subdirectory: statistics
-- Adding the c++    library subdirectory: SamMD
-- Adding the c++    library subdirectory: SamMD2Export
-- Adding the c++    library subdirectory: eland_ms
-- Adding the c++    library subdirectory: kagu
-- Adding the c++    library subdirectory: smallRna
-- Adding the c++    program subdirectory: bin
-- Adding the c++    program subdirectory: Alignment
-- Adding the c++    program subdirectory: BaseCalls
-- Adding the c++    program subdirectory: PostAlignment
-- Adding the c++    program subdirectory: Demultiplex
-- Adding the c++    program subdirectory: SmallRna
-- Doxygen: /usr/bin/doxygen. Dot: /usr/bin/dot.
-- Creating Doxygen config file: /home/john/Downloads/cassava/CASAVA_v1.8.2-build/c++/Doxyfile
-- Adding the verifyBoost dynamic link binary checker: verifyBoost
-- Found PTHREAD  header: /usr/include/pthread.h
-- Found PTHREAD library: /usr/lib64/libpthread.so
-- pthread supported
-- Configuring done
-- Generating done
-- Build files have been written to: /home/john/Downloads/cassava/CASAVA_v1.8.2-build
The build directory /home/john/Downloads/cassava/CASAVA_v1.8.2-build was configured successfully

Type make at the top level of the root directory to build CASAVA

[CASAVA_v1.8.2-build]$ make
[  0%] Extracting the CodeMin headers and examples
[  1%] Built target CASAVA_CODE_MIN
[  1%] Built target CASAVA_SAMTOOLS
[  1%] Building illumina_samtools_extensions
[  1%] Built target CASAVA_ILMNSAMTOOLS
[  1%] Unpacking merge.xslt
[  2%] Built target CASAVA_MERGE_XSLT
[  2%] Extracting the Chart director library and tools
[  2%] Built target CASAVA_CHART_DIRECTOR
[  2%] Built target CASAVA_OPT
[ 12%] Built target casava_blt_util
[ 19%] Built target casava_blt_common
[ 20%] Built target casava_blt
[ 32%] Built target casava_starling
[ 45%] Built target casava_common
[ 46%] Built target casava_io
[ 50%] Built target casava_alignment
[ 51%] Built target casava_basecalling
[ 51%] Built target casava_assembly
[ 58%] Built target casava_variance
[ 58%] Building CXX object c++/lib/applications/CMakeFiles/casava_applications.dir/AlignContig.cpp.o
/home/john/Downloads/cassava/CASAVA_v1.8.2/src/c++/lib/applications/AlignContig.cpp: In member function ‘int ca::applications::AlignContig::run()’:
/home/john/Downloads/cassava/CASAVA_v1.8.2/src/c++/lib/applications/AlignContig.cpp:569:87: error: conversion from ‘boost::filesystem::path’ to non-scalar type ‘std::string {aka std::basic_string<char>}’ requested
make[2]: *** [c++/lib/applications/CMakeFiles/casava_applications.dir/AlignContig.cpp.o] Error 1
make[1]: *** [c++/lib/applications/CMakeFiles/casava_applications.dir/all] Error 2
make: *** [all] Error 2


[CASAVA_v1.8.2-build]$ uname -a
Linux mordor7 3.9.11-200.fc18.x86_64 #1 SMP Mon Jul 22 21:04:50 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

[sklages]

It is now called bcl2fastq, http://support.illumina.com/download...tware_184.ilmn

Just give it a try and see if installation works for you.

Software ships with boost 1.44; you should use that. Newer versions of boost may or may not be compatible with bcl2fastq/casava. I ran into such problems .. :-)

[john789]

Thanks sklages, it seems to have installed from the rpm without issue.

[georgeg9]

i found out that the problem was my gcc version(4.7.3) and i had to use an older one(4.4.7)

[GenoMax]

Btw, why 1.8.2? Current version is 1.8.4 (OK, without Eland/SNP caller).

One point to note. With 1Tb HiSeq 2500 upgrade (V4 reagents) the default option now uses compressed bcl files (gzipped). Bcl2fastq (v. 1.8.4) can handle these natively. If you wish to use CASAVA (v.1.8.2) you will have to decompress the BCL files manually.