HTSlib¶
Installing HTSlib¶
Standard installation¶
Probably, the easiest way to install htslib
is through your package
manager. But it can be installed from sources; have a look at the
HTSlib webpage.
Spack¶
Another nice and simple possibility is to use Spack, particularly if you are going to work on a cluster where using its package manager is cumbersome, or even impossible. In this case the installation goes as follows.
(Optional) Choosing the compiler.
HTSlib
will be compiled from source code bySpack
. You might need to choose an up-to-date compiler (clusters tend to have very stable, ie. old, default compilers). See Using Spack for details.Installing
HTSlib
itself. With the default compiler it would be:$ spack install htslib
or if we want to install it with a specific compiler, say
gcc-11.3
:$ spack install htslib%gcc@11.3
Using
HTSlib
. PacBio Data Processing depends onHTSlib
at runtime. It means that after a successfull installation, the created module must be loaded whenever it is needed:$ module load htslib-1.9-gcc-11.3.0-gcc-8.2.0-qynjstf
Warning
Remember to add that line at the beginning of the slurm batch scripts used to submit any executable from PacBio Data Processing.