./kallisto: error while loading shared libraries: libhdf5.so.7: cannot open shared object file:

[stephenturner]

I built HDF5 as instructed, (but not in my home directory). Added the lib directory to LD_LIBRARY_PATH.

Running kallisto gives me the error ./kallisto: error while loading shared libraries: libhdf5.so.7: cannot open shared object file: No such file or directory

I solved this by going into /path/to/hdf5-1.8.15-patch1/lib and running ln -s libhdf5.so libhdf5.so.7. Not sure if others have experienced this, but this worked for me.

[jvivian]

Thanks for the fix @stephenturner, I had this same issue when building Kallisto into a Docker container.

[mschilli87]

I also built HDF5 locally (from source version 1.8.15) and invoke kallisto using LD_LIBRARY_PATH=/hdf5/lib/path:$LD_LIBRARY_PATH kallisto without any library loading problems.

[matrs]

I just had this problem (08-2017, more recent hdf5 version involved) and I thought that if I remove and install again kallisto, it should use the hdf5 currently installed in my system, which wasn't the version kallisto was expecting. That worked and the problem was fixed.
I think all the packages that use a x library should know when that x library gets updated and rebuild against that new version if possible, or complain. Probably this doesn't usually happen and this is a particular problem with this package, because automatic dependency resolution is one of the main points of using a package manager.