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On 2 Oct 2020, at 10:45, Andreas Tille <<a href="mailto:andreas@fam-tille.de" class="">andreas@fam-tille.de</a>> wrote:<br class="">
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<div class="">Please inspect<br class="">
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<a href="https://salsa.debian.org/med-team/htslib/-/commit/88644ba8e4096302d996dae2a0399195e2e53819" class="">https://salsa.debian.org/med-team/htslib/-/commit/88644ba8e4096302d996dae2a0399195e2e53819</a><br class="">
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<div>That is the right place for configure options.</div>
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<div class="">(and also your hint to the pull request<br class="">
<a href="https://salsa.debian.org/med-team/htslib/-/commit/84fcfcfda2b0b89d743bc8adb617abdf5cc22d4b" class="">https://salsa.debian.org/med-team/htslib/-/commit/84fcfcfda2b0b89d743bc8adb617abdf5cc22d4b</a> )<br class="">
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<div>That looks correct.</div>
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<blockquote type="cite" class="">See HTSlib's INSTALL file for details. Packagers such as yourselves should set with-plugin-path thus so that plugins in both /usr/local and /usr will be used; If Debian still folds /usr/libexec into /usr/lib or nearby, you may
wish to adjust both --with-plugin-dir and --with-plugin-path.<br class="">
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I guess you mean that I need to make sure that<br class="">
plugindir=/usr/lib/htslib<br class="">
right?</div>
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<div>There is no need to patch configure.ac to alter this. Just add --with-plugin-dir='$(libdir)/htslib' as another configure option.</div>
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<div>I see Debian policy at last now blesses FHS 3.0, which includes libexec. However you may not wish to be in the vanguard of this, so that /usr/lib/ARCH/htslib would indeed appear to be the existing-Debian-style appropriate place under /usr. For /usr/local,
any third-party instructions are likely to recommend installing their plugin into /usr/local/libexec/htslib, so I would recommend configuring with</div>
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<div><span class="Apple-tab-span" style="white-space:pre"></span>--enable-plugins --with-plugin-dir='$(libdir)/htslib' --with-plugin-path='/usr/local/lib/htslib:/usr/local/libexec/htslib:$(plugindir)'</div>
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<div>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.)</div>
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<div>BTW it looks like <span style="font-size: 13px;" class="">htslib-s3-plugin.7.gz has ben placed in libhts3 basically by default, although that is the right package for it. IMHO that would also be the right package for man5/*.5.gz as these are </span><span style="font-size: 13px;" class="">man
pages aimed at users (not just developers) but YMMV.</span></div>
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<div class="">How can I verify / test the correct setting?<br class="">
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<div class="">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`.</div>
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<div class="">Cheers,</div>
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<div class=""> John</div>
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