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wtsi-npg / bambi

Process Illumina instrument data into SAM/BAM/CRAM files.
http://wtsi-npg.github.io/bambi
GNU Affero General Public License v3.0
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Configuration improvements #173

Closed jenniferliddle closed 3 years ago

jenniferliddle commented 3 years ago

Try to make the configuration more robust, and make the presence of libgd optional.

Fixes issues #170, #167, #163

jenniferliddle commented 3 years ago

@jkbonfield : thanks for your comments. I have taken your advice about finding the htslib version, and I have restored the list of libraries to link with so that it will work with a statically linked htslib as well as a dynamically linked one.

I'm also taking your advice to avoid pkg-config :-)

What I have now isn't perfect, but I think it's an improvement on the original. If you agree, and can't find any problems with it, could I ask you to hit the merge button?

jkbonfield commented 3 years ago

I'm still not convinced it works properly with all possible static htslib libraries yet, but to be honest it's a bit of a rare scenario and as you say it's definitely an improvement on the original and several steps forward is better than none at all. Thanks for the updates.

Edit: forgot to say, I don't think I have permission to do the merge, but feel free to take this is an acceptance for you to click the button. :)