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CSB5 / lofreq

LoFreq Star: Sensitive variant calling from sequencing data
http://csb5.github.io/lofreq/
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HTSLIB Variable #138

Open mkadlof opened 9 months ago

mkadlof commented 9 months ago

Hi,

What's is wrong with passing value of --with-htslib with ${HTSLIB}?

https://github.com/CSB5/lofreq/blob/54281cd875821257adfd92baa957c13d96fa58c5/configure.ac#L193

andreas-wilm commented 9 months ago

Hello, it's a requirement of m4/ax_with_htslib.m4, which I'm using here.

mkadlof commented 8 months ago

I understand your point. May I suggest that it's worth considering a message change? The current message might give the impression that an absolute path is required, but in reality, the path can be provided using a variable with a different name, such as ${HTSLIB_PATH} or something similar. This aspect wasn't immediately intuitive to me, and I encountered some difficulties as a result.

I'm currently in the process of building a Docker container, and being able to pass paths via variables is quite valuable.