debian/README.test

+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+    sh run-unit-test
+
+in order to confirm its integrity.

debian/control

@@ -17,6 +17,7 @@ Depends: ${shlibs:Depends},
          ${misc:Depends},
          python,
          lagan
+Suggests: sibelia-examples
 Description: comparative genomics tool
  Sibelia (Synteny Block ExpLoration tool) is a comparative genomics tool:
  It assists biologists in analysing the genomic variations that correlate
@@ -30,3 +31,43 @@ Description: comparative genomics tool
   1) shared regions,
   2) regions that present in one group of genomes but not in others,
   3) rearrangements that transform one genome to other genomes.
+
+Package: sibelia-examples
+Architecture: all
+Depends: ${misc:Depends},
+Description: comparative genomics tool (example data)
+ Sibelia (Synteny Block ExpLoration tool) is a comparative genomics tool:
+ It assists biologists in analysing the genomic variations that correlate
+ with pathogens, or the genomic changes that help microorganisms adapt in
+ different environments. Sibelia will also be helpful for the
+ evolutionary and genome rearrangement studies for multiple strains of
+ microorganisms.
+ .
+ Sibelia is useful in finding:
+ .
+  1) shared regions,
+  2) regions that present in one group of genomes but not in others,
+  3) rearrangements that transform one genome to other genomes.
+ .
+ This package contains example data for sibelia.
+
+Package: sibelia-annotate
+Architecture: all
+Depends: ${misc:Depends},
+         python,
+         openjdk-11-jre | default-jre
+Description: comparative genomics tool (annotation tool using snpEFF)
+ Sibelia (Synteny Block ExpLoration tool) is a comparative genomics tool:
+ It assists biologists in analysing the genomic variations that correlate
+ with pathogens, or the genomic changes that help microorganisms adapt in
+ different environments. Sibelia will also be helpful for the
+ evolutionary and genome rearrangement studies for multiple strains of
+ microorganisms.
+ .
+ Sibelia is useful in finding:
+ .
+  1) shared regions,
+  2) regions that present in one group of genomes but not in others,
+  3) rearrangements that transform one genome to other genomes.
+ .
+ This package contains an annotation tool using snpEFF.

debian/createmanpages

@@ -30,7 +30,10 @@ help2man --no-info --no-discard-stderr \
             --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
 echo $AUTHOR >> $MANDIR/${progname}.1
 
-echo "$MANDIR/*.1" > debian/manpages
+cat > debian/sibelia.manpages <<EOT
+debian/C*.1
+debian/S*.1
+EOT
 
 cat <<EOT
 Please enhance the help2man output.

debian/manpages

-debian/*.1

debian/rules

@@ -10,13 +10,15 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 %:
 	dh $@ --sourcedirectory=src
 
-override_dh_installdocs:
-	dh_installdocs
-	mv debian/$(DEB_SOURCE)/usr/share/Sibelia/doc/* debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)
-	rmdir debian/$(DEB_SOURCE)/usr/share/Sibelia/doc
-	dh_link usr/share/doc/$(DEB_SOURCE) usr/share/Sibelia/doc
-
 override_dh_install:
 	dh_install
 	find debian -name LICENSE.txt -delete
 	find debian -name INSTALL.md -delete
+
+override_dh_installman:
+	dh_installman
+	mkdir -p debian/$(DEB_SOURCE)-annotate//usr/share/man/man1
+	mv debian/$(DEB_SOURCE)-annotate/usr/share/man/py/man1/snpEffAnnotate.1 debian/$(DEB_SOURCE)-annotate/usr/share/man/man1/snpEffAnnotate.py.1
+	rm -rf debian/$(DEB_SOURCE)-annotate/usr/share/man/py/
+	mv debian/$(DEB_SOURCE)/usr/share/man/py/man1/C-Sibelia.1 debian/$(DEB_SOURCE)/usr/share/man/man1/C-Sibelia.py.1
+	rm -rf debian/$(DEB_SOURCE)/usr/share/man/py

debian/sibelia-annotate.install

+usr/bin/snpEffAnnotate.py
+usr/lib/Sibelia/snpEff

debian/lintian-overrides → debian/sibelia-annotate.lintian-overrides

 # see https://lists.debian.org/debian-med/2018/06/msg00043.html
-sibelia: script-with-language-extension usr/bin/*.*
+sibelia-annotate: script-with-language-extension usr/bin/*.*
 # this file should not be there in an official package - so just ignore the wrong place for now
-sibelia: jar-not-in-usr-share usr/lib/Sibelia/snpEff/snpEff.jar
+sibelia-annotate: jar-not-in-usr-share usr/lib/Sibelia/snpEff/snpEff.jar

debian/sibelia-annotate.manpages

+debian/snpEffAnnotate.py.1

debian/sibelia-examples.install

+usr/share/Sibelia/doc/examples	usr/share/doc/sibelia/

debian/sibelia.docs

+usr/share/Sibelia/doc/[A-Z]*
+debian/README.test
+debian/tests/run-unit-test

debian/sibelia.install

+usr/bin/C*
+usr/bin/S*
+usr/share/Sibelia/utils

debian/sibelia.links

+usr/share/doc/sibelia	usr/share/Sibelia/doc

debian/sibelia.lintian-overrides

+# see https://lists.debian.org/debian-med/2018/06/msg00043.html
+sibelia: script-with-language-extension usr/bin/*.*

debian/sibelia.manpages

+debian/C*.1
+debian/S*.1

debian/tests/control

+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr

debian/tests/run-unit-test

+#!/bin/bash
+set -e
+
+pkg=sibelia
+
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
+
+cd $AUTOPKGTEST_TMP
+gunzip -r *
+
+cd C-Sibelia/Staphylococcus_aureus
+C-Sibelia.py NCTC8325.fasta RN4220.fasta
+
+cd $AUTOPKGTEST_TMP/Sibelia/Helicobacter_pylori
+Sibelia -s loose Helicobacter_pylori.fasta