Installing Bam-Readcount

Question

[waihungh]

I'm installing bam-readcount for my analysis. However, when I came to the last step in executing the command "make", error appeared as:

bamreadcount.cpp:4:17: fatal error: sam.h: No such file or directory compilation terminated.

make[2]: * [build/src/exe/bam-readcount/CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o] Error 1

make[1]: * [build/src/exe/bam-readcount/CMakeFiles/bam-readcount.dir/all] Error 2

make: * [all] Error 2

Could anyone advice on how to proceed?

Thanks

Answer 1

[ron_veg]

Hi,

I'm trying to install bam-readcount too. I followed the instructions but i keep getting an error at the last step: 'make' after the cmake command. Until that everything works fine.

The error appears as:

/home/schwessi/samtools-0.1.19/libbam.a(bgzf.o): In function `bgzf_mt':
/home/schwessi/samtools-0.1.19/bgzf.c:445: undefined reference to `pthread_create'
/home/schwessi/samtools-0.1.19/libbam.a(bgzf.o): In function `mt_destroy':
/home/schwessi/samtools-0.1.19/bgzf.c:458: undefined reference to `pthread_join'
collect2: ld returned 1 exit status
make[2]: *** [bin/bam-readcount] Error 1
make[1]: *** [build/src/exe/bam-readcount/CMakeFiles/bam-readcount.dir/all] Error 2
make: *** [all] Error 2

Any advice would be nice.

Thanks
Ron

[tgi.tabbott]

I updated the code to always link the platform threading library (pthreads on linux), so this shouldn't be an issue in the future.

[ron_veg]

Nevermind, fixed the problem. Apparently the installion doesnt work with samtools 0.1.19. Tried 0.1.17 and it worked.

[nnutter]

Thanks for letting us know. I'll update the README to mention that 0.1.19 may not work.

Answer 2

[Cyriac Kandoth]

The error message is complaining that you have not included the samtools library header (sam.h). Follow these instructions, and see if they help.

[waihungh]

I have followed the instructions but seems have problem linking with samtools

[Cyriac Kandoth]

To help us troubleshoot, please provide more information:

• your operating system version
• the sequence of steps performed before running make

Answer 3

[waihungh]

It is ubuntu linux (Linux version 3.2.0-26-generic (buildd@batsu) (gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5) ) #41-Ubuntu SMP Thu Jun 14 17:49:24 UTC 2012).

I just follow the instruction of bam-readcount. After exporting SAMTOOLS_ROOT, I recursively clone the bam-readcount repository without error.

When I execute the cmake command, there was a warning:

WARNING: Target "bam-readcount" requests linking to directory "/software/sequencing/samtools_latest".  Targets may link only to libraries.  CMake is dropping the item.

When I further execute the make command, error appeared as:

[100%] Building CXX object build/src/exe/bam-readcount/CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o
/home/danielho/bam-readcount/src/exe/bam-readcount/bamreadcount.cpp:1:0: warning: "_GNU_SOURCE" redefined [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
/home/danielho/bam-readcount/src/exe/bam-readcount/bamreadcount.cpp:4:17: fatal error: sam.h: No such file or directory
compilation terminated.
make[2]: *** [build/src/exe/bam-readcount/CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o] Error 1
make[1]: *** [build/src/exe/bam-readcount/CMakeFiles/bam-readcount.dir/all] Error 2
make: *** [all] Error 2

[nnutter]

Can you append to your reply what you are setting SAMTOOLS_ROOT to and what the contents are, e.g. ls $SAMTOOLS_ROOT.

[waihungh]

export SAMTOOLS_root=/software/sequencing/samtools_latest

The contents are:

AUTHORS   ChangeLog  examples  Makefile        misc  samtools    win32
bcftools  COPYING    INSTALL   Makefile.mingw  NEWS  samtools.1

[nnutter]

I believe you should see sam.h in SAMTOOLS_ROOT so I suspect you may need to set it as, export SAMTOOLS_ROOT=/software/sequencing/samtools_latest/samtools.