Htslib plugins

[James Bonfield <jkb@sanger.ac.uk>]

The rules file for Htslib appear to use an undefined variable $(plugindir).

https://salsa.debian.org/med-team/htslib/-/blob/master/debian/rules

	dh_auto_configure -- --enable-libcurl --enable-gcs --enable-s3
	--enable-plugins --with-plugin-dir='$(libdir)/htslib'
	--with-external-htscodecs
	--with-plugin-path='/usr/local/lib/htslib:/usr/local/libexec/htslib:$(plugindir)'

Note the $(plugindir) at the end.  This doesn't seem to be specified
anywhere, and has caused a problem for one of our users.  This is
evidenced by running "samtools version" to dump out the current
configuration.

It would be a trivial fix to just copy the $(libdir)/htslib definition
supplied to --with-plugin-dir here instead of $(plugindir).  Or if we
do define plugindir somewhere, it should be passed into
--with-plugin-dir so at least the two definitions are in sync.

The consequence of this is that htslib can't find the plugins, and in
doing so misses out on fetching data via https, S3, GCS and other
protocols.  This has been verified by my colleague in this github issue:

https://github.com/samtools/htslib/issues/1515#issuecomment-1283876113

Regards,

James

PS.  This Salsa GitLab page is bugged for me, using firefox.  There's
no horizontal scrollbar until I scroll down to the bottom of the
screen. That's a very tedious way to scroll a web page right!  I just
cut and pasted it in the end.


-- 
James Bonfield (jkb@sanger.ac.uk)
The Sanger Institute, Hinxton, Cambs, CB10 1SA


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