debian/changelog

+ssake (4.0-2) unstable; urgency=medium
+
+  * Fix installation of tools
+  * Fix link in examples, Depends: ssake
+    Closes: #910414
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * Fix broken interpreter definitions
+  * Avoid errors when trying to fix shebang line in shell scripts
+
+ -- Andreas Tille <tille@debian.org>  Mon, 08 Oct 2018 09:04:43 +0200
+
 ssake (4.0-1) unstable; urgency=medium
 
   * New upstream version

debian/control

@@ -6,9 +6,9 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 11~),
                python-markdown
-Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/ssake.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/ssake.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/ssake
+Vcs-Git: https://salsa.debian.org/med-team/ssake.git
 Homepage: http://www.bcgsc.ca/platform/bioinfo/software/ssake
 
 Package: ssake
@@ -29,8 +29,8 @@ Description: genomics application for assembling millions of very short DNA sequ
 
 Package: ssake-examples
 Architecture: all
-Depends: ${misc:Depends}
-Suggests: ssake
+Depends: ${misc:Depends},
+         ssake
 Description: example data for SSAKE, a genomic assembler of short reads
  This package contains test sequences for SSAKE, a genomics application for
  assembling millions of very short DNA sequences.

debian/rules

@@ -16,13 +16,17 @@ DOCDIR := $(CURDIR)/debian/$(examples)/usr/share/doc/$(DEB_SOURCE)
 override_dh_install:
 	dh_install
 	cp -a SSAKE $(BINDIR)/ssake
-	cp -a tools/TQS.py $(BINDIR)/tqs
+	# Fix totally broken interpreter definitions
+	for pl in `grep -Rl '#!/home/.\+/perl' debian/*/usr/*` ; do \
+	    sed -i '1s?^#!/home/.\+/perl?#!/usr/bin/perl?' $${pl} ; \
+	done
+	for sh in `grep -Rl '#!/usr/bin/bash' debian/*/usr/*` ; do \
+	    sed -i '1s?^#!/usr/bin/bash?#!/bin/bash?' $${sh} ; \
+	done
 
 override_dh_installexamples:
 	dh_installexamples
-	for sh in $(DOCDIR)/examples/*.sh ; do \
-	    sed -i '1 i #!/bin/sh' $${sh} ; \
-	done
+	find $(DOCDIR)/examples -name "*.sh" -type f -exec sed -i '1 i #!/bin/sh' \{\} \;
 
 override_dh_installdocs:
 	dh_installdocs

debian/ssake-examples.links

+usr/share/ssake/runSSAKE.sh	usr/share/doc/ssake/examples/runSSAKE.sh

debian/ssake.docs

-tools/TQS.readme
+tools/*readme
+tools/*README

debian/ssake.install

-tools/[mn]*.pl     usr/share/ssake
+tools/*.pl     usr/share/ssake
+tools/*.py     usr/share/ssake
+tools/*.sh     usr/share/ssake

debian/ssake.links

+usr/share/ssake/TQS.py	usr/bin/tqs