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 ([email protected]) The Sanger Institute, Hinxton, Cambs, CB10 1SA -- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
