debian/changelog

+jellyfish (2.3.0-2) UNRELEASED; urgency=medium
+
+  * Restore jellyfish-examples, needed for the autopkgtest (Closes: #941262)
+  * Enable an additional two test categories in the autopkgtests
+  * Enabled htslib, to read SAM/BAM/CRAM files
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Fri, 27 Sep 2019 15:00:00 +0200
+
 jellyfish (2.3.0-1) unstable; urgency=medium
 
   * Team upload

debian/control

@@ -16,7 +16,10 @@ Build-Depends: debhelper-compat (= 12),
                python3-all-dev,
                dh-python,
                perl,
-               chrpath
+               chrpath,
+               libhts-dev,
+               dos2unix,
+               samtools
 Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/jellyfish
 Vcs-Git: https://salsa.debian.org/med-team/jellyfish.git
@@ -137,24 +140,24 @@ Description: count k-mers in DNA sequences (Perl bindings of jellyfish)
  .
  This package contains the Perl bindings of jellyfish.
 
-#Package: jellyfish-examples
-#Architecture: any
-#Depends: jellyfish,
-#         ${shlibs:Depends},
-#         ${misc:Depends}
-#Description: count k-mers in DNA sequences (examples for testing)
-# JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
-# DNA. A k-mer is a substring of length k, and counting the occurrences
-# of all such substrings is a central step in many analyses of DNA
-# sequence. JELLYFISH can count k-mers using an order of magnitude less
-# memory and an order of magnitude faster than other k-mer counting
-# packages by using an efficient encoding of a hash table and by
-# exploiting the "compare-and-swap" CPU instruction to increase
-# parallelism.
-# .
-# JELLYFISH is a command-line program that reads FASTA and multi-FASTA
-# files containing DNA sequences. It outputs its k-mer counts in an
-# binary format, which can be translated into a human-readable text
-# format using the "jellyfish dump" command.
-# .
-# This package contains examples to test the package
+Package: jellyfish-examples
+Architecture: any
+Depends: jellyfish,
+         ${shlibs:Depends},
+         ${misc:Depends}
+Description: count k-mers in DNA sequences (examples for testing)
+ JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
+ DNA. A k-mer is a substring of length k, and counting the occurrences
+ of all such substrings is a central step in many analyses of DNA
+ sequence. JELLYFISH can count k-mers using an order of magnitude less
+ memory and an order of magnitude faster than other k-mer counting
+ packages by using an efficient encoding of a hash table and by
+ exploiting the "compare-and-swap" CPU instruction to increase
+ parallelism.
+ .
+ JELLYFISH is a command-line program that reads FASTA and multi-FASTA
+ files containing DNA sequences. It outputs its k-mer counts in an
+ binary format, which can be translated into a human-readable text
+ format using the "jellyfish dump" command.
+ .
+ This package contains examples to test the package

debian/copyright

@@ -5,7 +5,7 @@ Source: http://www.cbcb.umd.edu/software/jellyfish/
 
 Files: *
 Copyright: Copyright 2011-2014 Guillaume Marçais1, Carl Kingsford
-License: GPL-3+
+License: GPL-3+ or BSD-3-clause
 
 Files: jellyfish/randomc.h
 Copyright: Copyright 2008 Agner Fog
@@ -71,6 +71,8 @@ Files: unit_tests/gtest/src/gtest_main.cc
        unit_tests/gtest/src/gtest-all.cc
        unit_tests/gtest/gtest.h
 Copyright: 2005-2008 Google Inc.
+License: BSD-3-clause
+
 License: BSD-3-clause
  Redistribution and use in source and binary forms, with or without
  modification, are permitted provided that the following conditions are

debian/jellyfish-examples.examples

 tests/*.sh*
 unit_tests/unit_tests.sh
+compat.sh

debian/patches/series

@@ -4,3 +4,4 @@ portability.patch
 #Apparently fixed upstream
 #fix_catch.patch
 fix_replacement_of_-L_option.patch
+test_needs_bash

debian/patches/test_needs_bash

+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Subject: small_mers needs bash
+
+Due to process substitution. Thanks to https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/jellyfish.html for highlighting this.
+--- jellyfish.orig/tests/small_mers.sh
++++ jellyfish/tests/small_mers.sh
+@@ -1,4 +1,4 @@
+-#! /bin/sh
++#! /bin/bash
+ 
+ cd tests
+ . ../compat.sh

debian/rules

@@ -10,6 +10,7 @@ export DH_OPTIONS
 export PKG_CONFIG_LIBDIR=${CURDIR}
 export PKG_CONFIG_ALLOW_SYSTEM_LIBS=true
 export PKG_CONFIG_SYSROOT_DIR=${CURDIR}/debian/tmp/
+export PKG_CONFIG_PATH=$(shell pkg-config --variable pc_path pkg-config)
 export PERL_MM_OPT=INSTALLDIRS=vendor
 export PYBUILD_BUILD_ARGS=build_ext --rpath "${CURDIR}/debian/tmp/usr/lib/${DEB_HOST_MULTIARCH}"
 
@@ -52,7 +53,7 @@ override_dh_install:
 	sed -i "/dependency_libs/ s/'.*'/''/" ./debian/libjellyfish-2.0-dev/usr/lib/${DEB_HOST_MULTIARCH}/*.la
 
 override_dh_auto_configure:
-	dh_auto_configure -- --enable-swig --enable-perl-binding # --enable-python-binding
+	dh_auto_configure -- --enable-swig --enable-perl-binding --enable-htslib # --enable-python-binding
 
 override_dh_clean:
 	dh_clean
@@ -87,3 +88,4 @@ override_dh_auto_build:
 # uncommenting the following.
 #override_dh_auto_test:
 #	BIG=1 dh_auto_test
+#	false

debian/tests/run-unit-test

@@ -8,7 +8,8 @@ fi
 cd $ADTTMP
 mkdir tests
 cp -a /usr/share/doc/jellyfish-examples/examples/* tests
-sed -i "s#DIR=../bin#DIR=/usr/lib/${pkg}/bin#" tests/compat.sh
+mv tests/compat.sh ./
+sed -i "s#DIR=../bin#DIR=/usr/lib/${pkg}/bin#" compat.sh
 tests/generate_sequence.sh
 sh tests/parallel_hashing.sh
 sh tests/merge.sh
@@ -33,4 +34,6 @@ sh tests/multi_file.sh
 #############################################################################################
 sh tests/bloom_counter.sh
 sh tests/large_key.sh
+sh tests/sam.sh
+bash tests/small_mers.sh
 /usr/lib/jellyfish/bin/test_all