Author: tille Date: 2013-11-27 12:23:53 +0000 (Wed, 27 Nov 2013) New Revision: 15289
Added: trunk/packages/seqan/trunk/debian/README.Debian trunk/packages/seqan/trunk/debian/seqan-apps.links Removed: trunk/packages/seqan/trunk/debian/seqan-apps.manpages Modified: trunk/packages/seqan/trunk/debian/changelog trunk/packages/seqan/trunk/debian/copyright trunk/packages/seqan/trunk/debian/rules trunk/packages/seqan/trunk/debian/seqan-apps.install Log: Make sure only needed exectuables will be installed as links in /usr/bin and document this in README.Debian; manpages (via help2man) only for binaries in /usr/bin Added: trunk/packages/seqan/trunk/debian/README.Debian =================================================================== --- trunk/packages/seqan/trunk/debian/README.Debian (rev 0) +++ trunk/packages/seqan/trunk/debian/README.Debian 2013-11-27 12:23:53 UTC (rev 15289) @@ -0,0 +1,50 @@ +SeqAn for Debian +================ + +Quoting upstream namely Manuel Holtgrewe <[email protected]> +in a private mail to Andreas Tille <[email protected]> and +Filippo Rusconi <[email protected]> at Wed, 27 Nov 2013 09:38:30 +0100: + + The SeqAn apps are a pretty diverse collection. Some are just simple + tools for Bioinformaticians, some are results from our research. The + tools should be useful for useful but from the research result, only + some are. I would suggest placing the following binaries in /usr/bin + since they are tools useful for and used by users/scientists: + + alf + gustaf + insegt + masai_indexer + masai_mapper + masai_output_pe + masai_output_se + mason + micro_razers + pair_align + rabema_build_gold_standard + rabema_evaluate + rabema_prepare_sam + razers + razers3 + sak + seqan_tcoffee + snp_store + splazers + stellar + tree_recon + + [list was sorted and wildcard expanded (masai_*, rabema_*) by + Andreas Tille] + + The other binaries could live happily in /usr/bin/seqan. If there is a + collision, one could prefix seqan_ to the binary name. + +According to this advise all binary applications are moved to +/usr/lib/seqan/bin and the ones mentioned above symlinked to /usr/bin. +Manpages were created using help2man for the symlinked binaried. + +If there are good reasons to provide any additional binary under /usr/bin +please file a bug report using `reportbug seqan` and let us know about +your preference. + + Modified: trunk/packages/seqan/trunk/debian/changelog =================================================================== --- trunk/packages/seqan/trunk/debian/changelog 2013-11-27 10:51:16 UTC (rev 15288) +++ trunk/packages/seqan/trunk/debian/changelog 2013-11-27 12:23:53 UTC (rev 15289) @@ -22,11 +22,12 @@ - cdbs -> dh - Need to rename /usr/bin/join to /usr/bin/seqan-join to avoid name clash with coreutils - * debian/seqan-apps.links -> seqan-apps.install: Install applications - directly to /usr/bin * debian/generate_manpages: use help2man to autogenerate manpages + * debian/README.Debian: Describe what apps go to /usr/bin and why + * debian/seqan-apps.links: Update apps that should go to /usr/bin + according to mail from upstream - -- Andreas Tille <[email protected]> Fri, 22 Nov 2013 10:06:25 +0100 + -- Andreas Tille <[email protected]> Wed, 27 Nov 2013 10:26:17 +0100 seqan (1.3.1-1) unstable; urgency=low Modified: trunk/packages/seqan/trunk/debian/copyright =================================================================== --- trunk/packages/seqan/trunk/debian/copyright 2013-11-27 10:51:16 UTC (rev 15288) +++ trunk/packages/seqan/trunk/debian/copyright 2013-11-27 12:23:53 UTC (rev 15289) @@ -1,6 +1,7 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Contact: Manuel Holtgrewe <[email protected]> Hannes Röst <[email protected]> +Upstream-Name: SeqAn Source: http://packages.seqan.de/seqan-src/seqan-src-1.4.1.tar.gz Files: * Modified: trunk/packages/seqan/trunk/debian/rules =================================================================== --- trunk/packages/seqan/trunk/debian/rules 2013-11-27 10:51:16 UTC (rev 15288) +++ trunk/packages/seqan/trunk/debian/rules 2013-11-27 12:23:53 UTC (rev 15289) @@ -15,9 +15,10 @@ override_dh_install: dh_install - # /usr/bin/join is part of coreutils package: Avoid name conflict - # by renaming it to seqan-join - mv $(CURDIR)/debian/seqan-apps/usr/bin/join $(CURDIR)/debian/seqan-apps/usr/bin/seqan-join + # /usr/bin/join is part of coreutils package: Avoid name conflict by renaming it to seqan-join + # This solution is withdrawn in favour of just providing a set of binaries according to upstream + # in /usr/bin (via symlink) while others go to /usr/lib/seqan/bin (see README.Debian) + # mv $(CURDIR)/debian/seqan-apps/usr/bin/join $(CURDIR)/debian/seqan-apps/usr/bin/seqan-join # # Formerly binaries were installed into usr/lib/sequan/bin/ # and only some of them were made available in /usr/bin via dh_link @@ -51,7 +52,10 @@ fi rm -rf orig -override_dh_installman: +override_dh_link: + dh_link + # we generate only those manpages where binaries are linked to /usr/bin + # since dh_link is executed after dh_installmanpages this is done here $(CURDIR)/debian/generate_manpages get-orig-source: Modified: trunk/packages/seqan/trunk/debian/seqan-apps.install =================================================================== --- trunk/packages/seqan/trunk/debian/seqan-apps.install 2013-11-27 10:51:16 UTC (rev 15288) +++ trunk/packages/seqan/trunk/debian/seqan-apps.install 2013-11-27 12:23:53 UTC (rev 15289) @@ -1,2 +1,2 @@ -usr/bin/* usr/bin +usr/bin usr/lib/sequan usr/share/doc/* usr/share/doc/seqan-apps Added: trunk/packages/seqan/trunk/debian/seqan-apps.links =================================================================== --- trunk/packages/seqan/trunk/debian/seqan-apps.links (rev 0) +++ trunk/packages/seqan/trunk/debian/seqan-apps.links 2013-11-27 12:23:53 UTC (rev 15289) @@ -0,0 +1,21 @@ +usr/lib/sequan/bin/alf usr/bin/alf +usr/lib/sequan/bin/gustaf usr/bin/gustaf +usr/lib/sequan/bin/insegt usr/bin/insegt +usr/lib/sequan/bin/masai_indexer usr/bin/masai_indexer +usr/lib/sequan/bin/masai_mapper usr/bin/masai_mapper +usr/lib/sequan/bin/masai_output_pe usr/bin/masai_output_pe +usr/lib/sequan/bin/masai_output_se usr/bin/masai_output_se +usr/lib/sequan/bin/mason usr/bin/mason +usr/lib/sequan/bin/micro_razers usr/bin/micro_razers +usr/lib/sequan/bin/pair_align usr/bin/pair_align +usr/lib/sequan/bin/rabema_build_gold_standard usr/bin/rabema_build_gold_standard +usr/lib/sequan/bin/rabema_evaluate usr/bin/rabema_evaluate +usr/lib/sequan/bin/rabema_prepare_sam usr/bin/rabema_prepare_sam +usr/lib/sequan/bin/razers usr/bin/razers +usr/lib/sequan/bin/razers3 usr/bin/razers3 +usr/lib/sequan/bin/sak usr/bin/sak +usr/lib/sequan/bin/seqan_tcoffee usr/bin/seqan_tcoffee +usr/lib/sequan/bin/snp_store usr/bin/snp_store +usr/lib/sequan/bin/splazers usr/bin/splazers +usr/lib/sequan/bin/stellar usr/bin/stellar +usr/lib/sequan/bin/tree_recon usr/bin/tree_recon Deleted: trunk/packages/seqan/trunk/debian/seqan-apps.manpages =================================================================== --- trunk/packages/seqan/trunk/debian/seqan-apps.manpages 2013-11-27 10:51:16 UTC (rev 15288) +++ trunk/packages/seqan/trunk/debian/seqan-apps.manpages 2013-11-27 12:23:53 UTC (rev 15289) @@ -1,7 +0,0 @@ -debian/dfi.1 -debian/micro_razers.1 -debian/pair_align.1 -debian/razers.1 -debian/seqan_tcoffee.1 -debian/seqcons.1 -debian/tree_recon.1 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
