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Posted by bastien


I’m trying to install to install the sra-toolkit from the source (I couldn’t find it in solus repository) following these instructions:

Among others, the sra-toolkit depends on libhdf5. I couldn’t find libhdf5 in the repo so I tried to build it from source. I did so in my Downloads folder, which was probably not the smartest thing to do since sra-toolkit can’t find that library when I run sudo make install in sra-toolkit directory. I get this error: NOTE – pacbio-load cannot be built: It requires our internal library ‘libkdf5’ which requires ‘libhdf5’ and its development headers.

I tried to add the libhdf5 path to PATH and LD_LIBRARY_PATH using

export PATH=$PATH:~/Downloads/hdf5-1.10.4
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:~/Downloads/hdf5-1.10.4

but it didn’t work. Any idea of how to get sra-toolkit find libhdf5?

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1 Answer

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I did not succeed too. But you can turn around by installing it using bioconda:
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