debian/README.Debian

+sibelia for Debian
+==================
+
+Due to removal of the binary JAR of snpEff from the Debian package
+source the annotation feature is not available.  The removal was needed
+to enable uploading sibelia to Debian main.  If you really need the
+annotation feature via snpEff there are two options:
+
+  1. Help packaging snpEff from source.  The process had started in Git
+       https://salsa.debian.org/med-team/snpeff
+  2. Ask for creating a separate package sibelia-annotation that needs
+     to got to non-free.
+     
+
+ -- Andreas Tille <tille@debian.org>  Thu, 14 Feb 2019 14:52:05 +0100
+

debian/changelog

-sibelia (3.0.7+ds-1) UNRELEASED; urgency=medium
+sibelia (3.0.7+dfsg-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #<bug>)
-    As long as we have no official snpeff package I do not intend to
-    package this.
 
  -- Andreas Tille <tille@debian.org>  Thu, 14 Feb 2019 14:52:05 +0100

debian/control

@@ -51,23 +51,23 @@ Description: comparative genomics tool (example data)
  .
  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.
+#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/copyright

@@ -3,17 +3,14 @@ Upstream-Name: SiBELia
 Source: https://sourceforge.net/projects/sibelia-bio/files/
 Files-Excluded: */libdivsufsort*
                 */lagan
+                */snpEff
+Comment: Due to removal of snpEff the annotation feature is not available.
 
 Files: *
 Copyright: 2011-2018 Saint-Petersburg Academic University
                      Ilya Minkin, Nikolay Vyahhi, Mikhail Kolmogorov, Son Pham
 License: GPL-2
 
-Files: src/annotation/snpEff/*
-Copyright: © 2008-2016, Pablo Cingolani <pcingola@users.sourceforge.net>
-License: Apache-2.0 or BSD or LGPL-2 or LGPL-2.1
-Comment: Unfortunately that's a binary JAR which is not packaged from source
-
 Files: debian/*
 Copyright: 2019 Andreas Tille <tille@debian.org>
 License: GPL-2

debian/createmanpages

@@ -24,11 +24,11 @@ help2man --no-info --no-discard-stderr \
             --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
 echo $AUTHOR >> $MANDIR/${progname}.1
 
-progname=snpEffAnnotate.py
-help2man --no-info --no-discard-stderr \
-         --name="Script for variants annotation" \
-            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
-echo $AUTHOR >> $MANDIR/${progname}.1
+#progname=snpEffAnnotate.py
+#help2man --no-info --no-discard-stderr \
+#         --name="Script for variants annotation" \
+#            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+#echo $AUTHOR >> $MANDIR/${progname}.1
 
 cat > debian/sibelia.manpages <<EOT
 debian/C*.1

debian/patches/series

 use_debian_packaged_libdivsufsort.patch
 use_debian_packaged_lagan.patch
+snpeff_is_removed.patch

debian/patches/snpeff_is_removed.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Thu, 14 Feb 2019 14:52:05 +0100
+Description: snpEff is removed - see README.Debian
+
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -28,8 +28,6 @@ else()
+ 	if(NOT ONLY_SIBELIA)
+ 		include(ExternalProject)
+ 		install(PROGRAMS csibelia/C-Sibelia.py DESTINATION bin)
+-		install(PROGRAMS annotation/snpEffAnnotate.py DESTINATION bin)
+-		install(DIRECTORY annotation/snpEff DESTINATION ${LIB_DIR})
+ 		install(DIRECTORY utils DESTINATION ${SHARE_DIR})
+ 		install(DIRECTORY ${SOURCE_DIR} DESTINATION ${LIB_DIR} FILE_PERMISSIONS USE_SOURCE_PERMISSIONS DIRECTORY_PERMISSIONS USE_SOURCE_PERMISSIONS REGEX "${SOURCE_DIR}/Readmes|Makefile|${SOURCE_DIR}/src" EXCLUDE)
+ 	endif()

debian/rules

@@ -17,8 +17,8 @@ override_dh_install:
 
 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/
+#	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/tests/run-unit-test

@@ -13,6 +13,7 @@ cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
 cd $AUTOPKGTEST_TMP
 gunzip -r *
 
+set -x
 cd C-Sibelia/Staphylococcus_aureus
 C-Sibelia.py NCTC8325.fasta RN4220.fasta
 

debian/watch

 version=4
 
-opts="repacksuffix=+ds,dversionmangle=auto,repack,compression=xz" \
+opts="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \
   http://sf.net/sibelia-bio/Sibelia@ANY_VERSION@-Source@ARCHIVE_EXT@