[Debian-med-packaging] Bug#971542: Please enable HTSlib plugins

[Andreas Tille]

On Wed, Oct 07, 2020 at 09:36:06AM +0000, John Marshall wrote:
> 
> There is no need to patch configure.ac to alter this. Just add --with-plugin-dir='$(libdir)/htslib' as another configure option.
> 
> I see Debian policy at last now blesses FHS 3.0, which includes libexec. However you may not wish to be in the vanguard of this, so that /usr/lib/ARCH/htslib would indeed appear to be the existing-Debian-style appropriate place under /usr. For /usr/local, any third-party instructions are likely to recommend installing their plugin into /usr/local/libexec/htslib, so I would recommend configuring with
> 
> --enable-plugins --with-plugin-dir='$(libdir)/htslib' --with-plugin-path='/usr/local/lib/htslib:/usr/local/libexec/htslib:$(plugindir)'

OK, that's in Git now
 
> as being the most flexible for your users. (These directories are just scanned for files matching hfile_*.so; it is not an error if any of them does not exist.)
> 
> BTW it looks like htslib-s3-plugin.7.gz has ben placed in libhts3 basically by default, although that is the right package for it.

Sorry, I do not understand this sentence.

> IMHO that would also be the right package for man5/*.5.gz as these are man pages aimed at users (not just developers) but YMMV.

Done in Git.

> How can I verify / test the correct setting?

What exactly do you mean?  Test my lastest changes I mentioned above or
rather testing the package that is in unstable currently?
 
> By observing the -DPLUGINPATH=… setting that goes past in the log when plugin.c is compiled; by running `strings` on libhts.so; or by seeing what directories are scanned via e.g. `strace htsfile foo:bar 2>&1|grep O_DIRECTORY`.

Sorry, I do not understand what you want to express / want me to change.

Thanks a lot for your helpful hints

       Andreas.

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