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bam-readcount installation error
0
Entering edit mode
13 months ago
hsbinf • 20

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
bam-readcount • 1.1k views
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Entering edit mode
14 months ago
h.mon 25k
Brazil

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
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0
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Thanks a lot ! It works now

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0
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11 weeks ago
ATpoint 17k
Germany

Did you even read the installation instructions?

bam-readcount does not support in source builds. Create a new build directory, enter it, and run:

cd bam-readcount
mkdir repo && cmake ./repo 
make

The binary can then be found in the bin/ subdirectory of your build directory.

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0
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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?

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