Cannot install ATHLATES, issues with bamtools
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5.6 years ago

I am trying to install Athlates (July 31, 2014 version) from the instruction here: https://hpc.nih.gov/docs/Athlates.pdf on a computing cluster. However, I am running into issues with the corresponding bamtools. The Athlates makefile echoes the following command:

/usr/bin/g++ -O3 -I/n/home05/aewhatley/bamtools/include/ -L/n/home05/aewhatley/bamtools/lib *.cpp -o ../bin/typing -lpthread -lbamtools -lz

However, after installing bamtools (instructions here: https://github.com/pezmaster31/bamtools/wiki/Building-and-installing), there are no files present in the "/n/home05/aewhatley/bamtools/lib" folder that the command is trying to reach, and there is no "/n/home05/aewhatley/bamtools/include/" folder at all!

Has bamtools been changed since Athlates was created, and if so, how would I install it now? Thanks.

software error • 1.8k views
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If you followed bamtools install instructions, it is "installed" where you downloaded, unpacked and compiled it. So you should set LD_LIBRARY_PATH to point to the lib folder where you compiled bamtools:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/bamtools/lib

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I'm aware of that. The issue is that the Athlates installation is failing, and that appears to be because the files are not in the right place, as the include directory does not exist, and the lib directory is empty. Sorry if that was not clear from the OP. I'm asking if anyone knows why this is happening, and how to fix it.

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You mean bamtools is not compiling? So you should troubleshoot installing bamtools first.

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No, sorry, I meant the Athlates installation. I updated the previous comment.

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I'm also having the same problem. I even changed the line #include "api/BamReader.h" in the src/bam_manip.h file to the correct path of BamReader.h of bamtools. Still doesn't work. It still says it can't find api/BamReader.h

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yeah I am also getting the same issue is this issue due to wrong path provided ?

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