bam-readcount installation error

Question

[hsbinf]

Hi All,

I am trying to run bam-readcount but I get the following error in the "make" step of the installation. I am using cmake v3.4.3

The commands I used are:

>git clone https://github.com/genome/bam-readcount.git 

>cmake bam-readcount/ 

> make

Error:
> [ 82%] Linking CXX executable ../../../../bin/bam-readcount
> 
> ../../../../vendor/samtools/libbam.a(bam_import.o): In function
> `__bam_get_lines':
> 
> /Users/hshah2/vendor/samtools/bam_import.c:76: undefined reference to
> `gzopen64'
> 
> ../../../../vendor/samtools/libbam.a(bam_import.o): In function
> `sam_open':
> 
> /Users/hshah2/vendor/samtools/bam_import.c:472: undefined reference to
> `gzopen64'
> 
> ../../../../vendor/samtools/libbam.a(bam_import.o): In function
> `sam_header_read2':
> 
> /Users/hshah2/vendor/samtools/bam_import.c:126: undefined reference to
> `gzopen64' 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

Answer 1

[h.mon]

The usual and recommended method for cmake builds is to create a build/ dir. It can be anywhere you want, in general I place it inside the source tree:

mkdir -p ~/src/bam-readcount
cd ~/src/bam-readcount/

# get bleeding edge source
git clone https://github.com/genome/bam-readcount.git
mkdir bam-readcount/build
cd bam-readcount/build/
cmake ../
make

# get stable release
curl -L https://github.com/genome/bam-readcount/archive/v0.8.0.tar.gz -o bam-readcount-0.8.0.tar.gz
tar -xzf bam-readcount-0.8.0.tar.gz
mkdir bam-readcount-0.8.0/build
cd bam-readcount-0.8.0/build/
cmake ../
make

[hsbinf]

Thanks a lot ! It works now

Answer 2

[ATpoint]

git clone https://github.com/genome/bam-readcount.git
cd bam-readcount
mkdir repo && cd repo && cmake ../
make

The binary is then in repo.

[hsbinf]

I had tried that too. Says it cannot find CMakeLists.txt

That is why I ran cmake on the ./bam-readcount.

Do I need to copy anything in ./repo?

[lovegenetics]

I am having the same problem like @hsbinf. It says the directory ./repo does not appear to contain CMakeLists.txt

[ATpoint]

Try again, updated my answer. By the way, the tool is almost a decade old, there are for sure newer alternatives for whatever you want to do.