debian/README.Debian

-diamond for Debian
-------------------
-
-There is a name conflict with 
-
-  diamond - smart data producer for Graphite graphing package
-
-The short story is: We are facing a name clash in the Free Software
-universe and we have to circumvent this somehow.  The Debian Med team
-deals with situation usually the following way:
-
-  1. The diamond executable resides in
-        /usr/lib/debian-med/bin/diamond
-     and can be either executed there or users can use
-  2. A symlink with the name
-        /usr/bin/diamond-aligner
-     which can be used alternatively
-
-If you want to use diamond right from the command line just set the
-PATH variable like
-
-  export PATH=/usr/lib/debian-med/bin:$PATH
-
-If a user creates a file
-
-    ${HOME}/.blends
-
-with the content
-
-# Add Blend names here which should prepend its bin dir to PATH
-debian-med
-
-the med-config package automatically adds this PATH to the users
-environment (when using bash).
-
- -- Andreas Tille <tille@debian.org>  Thu, 05 Jan 2017 10:33:38 +0100

debian/changelog

+diamond-aligner (0.9.29+dfsg-2) unstable; urgency=medium
+
+  [ Frédéric Bonnard ]
+  * Upstream 0.9.29 includes patch to build diamond-aligner on any
+    Closes: #942850
+
+  [ Andreas Tille ]
+  * Package diamond was removed from Debian so the name /usr/bin/diamond
+    can be used again
+  * Set upstream metadata fields: Bug-Database, Bug-Submit.
+
+ -- Andreas Tille <tille@debian.org>  Fri, 10 Jan 2020 13:50:28 +0100
+
 diamond-aligner (0.9.29+dfsg-1) unstable; urgency=medium
 
   * Team upload.

debian/links

-usr/lib/debian-med/bin/diamond			usr/bin/diamond-aligner
-usr/lib/debian-med/share/man/man1/diamond.1	usr/share/man/man1/diamond-aligner.1 
+usr/bin/diamond			usr/bin/diamond-aligner
+usr/share/man/man1/diamond.1.gz	usr/share/man/man1/diamond-aligner.1.gz
 

debian/patches/fix-unsigned-char-by-default-arches.patch

---- a/src/basic/score_matrix.cpp
-+++ b/src/basic/score_matrix.cpp
-@@ -36,7 +36,7 @@
- 
- const double INT2_MAX = std::numeric_limits<double>::max();
- 
--const char DNA_scores[5 * 5] = {
-+const signed char DNA_scores[5 * 5] = {
- 	2, -3, -3, -3, -3,
- 	-3,2,-3,-3,-3,
- 	-3,-3,2,-3,-3,
-@@ -317,4 +317,4 @@
- 	constants[3] = lambda;
- 	constants[4] = K;
- 	constants_ = constants;
--}
-\ No newline at end of file
-+}

debian/patches/series

 avoid_unwanted_optimisation.patch
 82feea2aee5c82e283704b9317cb5e8abc625f90.patch
-fix-unsigned-char-by-default-arches.patch

debian/rules

@@ -13,26 +13,8 @@ MSSSSE3=$(shell if [ `dpkg-architecture -qDEB_BUILD_ARCH` = 'amd64' ] ; then ech
 %:
 	dh $@
 
-override_dh_install:
-	dh_install
-	# due to a file name conflict diamond is moved out of the way
-	mkdir -p debian/$(DEB_SOURCE)/usr/lib/debian-med/bin/
-	mv debian/$(DEB_SOURCE)/usr/bin/diamond debian/$(DEB_SOURCE)/usr/lib/debian-med/bin/
-
-override_dh_installman:
-	dh_installman
-	# due to a file name conflict diamond.1 is moved out of the way
-	mkdir -p debian/$(DEB_SOURCE)/usr/lib/debian-med/share/man/man1/
-	mv debian/$(DEB_SOURCE)/usr/share/man/man1/diamond.1 debian/$(DEB_SOURCE)/usr/lib/debian-med/share/man/man1/
-	gzip -9 debian/$(DEB_SOURCE)/usr/lib/debian-med/share/man/man1/diamond.1
-
 override_dh_compress:
 	dh_compress --exclude=.pdf
 
-override_dh_fixperms:
-	dh_fixperms
-	# strangely the manpage becomes executable ... hmmm
-	chmod -x debian/$(DEB_SOURCE)/usr/lib/debian-med/share/man/man1/*
-
 build_simple:
 	MSSSSE3=$(MSSSSE3) build_simple.sh

debian/upstream/metadata

@@ -10,11 +10,13 @@ Reference:
   PMID: 25402007
   URL: http://www.nature.com/nmeth/journal/v12/n1/abs/nmeth.3176.html
 Registry:
-  - Name: OMICtools
-    Entry: OMICS_08011
-  - Name: bio.tools
-    Entry: Diamond
-  - Name: SciCrunch
-    Entry: SCR_016071
-  - Name: conda:bioconda
-    Entry: diamond
+- Name: OMICtools
+  Entry: OMICS_08011
+- Name: bio.tools
+  Entry: Diamond
+- Name: SciCrunch
+  Entry: SCR_016071
+- Name: conda:bioconda
+  Entry: diamond
+Bug-Database: https://github.com/bbuchfink/diamond/issues
+Bug-Submit: https://github.com/bbuchfink/diamond/issues/new