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odelaneau / shapeit4

Segmented HAPlotype Estimation and Imputation Tool
MIT License
89 stars 17 forks source link

Question about the static HTSlib library dependence #74

Closed ramiromagno closed 2 years ago

ramiromagno commented 2 years ago

Hi @odelaneau :

Thank you for developing such a terrific tool.

I am planning to install SHAPEIT4 in Arch Linux. I was checking the install instructions and I realised I need the libhts.a library installed.

I do have an Arch Linux package for htslib but it seems that the only libraries installed are the dynamic libraries .so:

$> pacman -Ql htslib | grep libhts
htslib /usr/lib/libhts.so
htslib /usr/lib/libhts.so.1.14
htslib /usr/lib/libhts.so.3

The Arch Linux package boost on the other hand does provide the static libraries you mention in the installation instructions.

$> pacman -Ql boost | grep -P 'libboost_(pro|io).+a$'
boost /usr/lib/libboost_iostreams.a
boost /usr/lib/libboost_program_options.a

So I am wondering if is my Arch package that is missing the static libraries for htslib or whether your installation instructions are perhaps not up to date... I don't really know.

As a side note, you have a typo in the installation instructions, libboost_iostreams.a is mentioned twice, when libboost_program_options.a should have been instead.

snap

ramiromagno commented 2 years ago

The issue was the packaging of htslib on the Arch: https://aur.archlinux.org/packages/htslib. It is solved now.