[med-svn] r15289 - trunk/packages/seqan/trunk/debian

Andreas Tille tille at moszumanska.debian.org
Wed Nov 27 12:23:53 UTC 2013 

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 <manuel.holtgrewe at fu-berlin.de>
+in a private mail to Andreas Tille <andreas at fam-tille.de> and
+Filippo Rusconi <lopippo at debian.org> 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 <tille at debian.org>  Fri, 22 Nov 2013 10:06:25 +0100
+ -- Andreas Tille <tille at debian.org>  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 <manuel.holtgrewe at fu-berlin.de>
                   Hannes Röst <roest at imsb.biol.ethz.ch>
+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

More information about the debian-med-commit mailing list