debian/atac.docs

 README.atac
 debian/tests/atac-unit-test
-debian/tests/test-data/test_data.tar.gz
 debian/README.test

debian/changelog

-kmer (0~20150903+r2013-6) UNRELEASED; urgency=medium
+kmer (0~20150903+r2013-6) unstable; urgency=medium
 
   * Team upload.
+
+  [ Liubov Chuprikova ]
   * Add autopkgtest.
   * Standards-Version: 4.2.1
   * Add a patch to fix wrong evaluation order in an expression
     Closes: #906980
 
+  [ Andreas Tille ]
+  * Provide test data in new package kmer-examples to avoid duplication of
+    data in two packages
+
  -- Liubov Chuprikova <chuprikovalv@gmail.com>  Mon, 27 Aug 2018 11:37:43 +0200
 
 kmer (0~20150903+r2013-5) unstable; urgency=medium

debian/control

@@ -93,7 +93,8 @@ Package: sim4db
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends}
-Recommends: leaff
+Recommends: leaff,
+            kmer-examples
 Description: batch spliced alignment of cDNA sequences to a target genome
  Sim4db performs fast batch alignment of large cDNA (EST, mRNA) sequence
  sets to a set of eukaryotic genomic regions. It uses the sim4 and sim4cc
@@ -124,6 +125,7 @@ Depends: ${shlibs:Depends},
          leaff,
          meryl,
          gnuplot
+Recommends: kmer-examples
 Description: genome assembly-to-assembly comparison
  atac computes a one-to-one pairwise alignment of large DNA sequences. It first
  finds the unique k-mers in each sequence, chains them to larger blocks, and
@@ -140,3 +142,17 @@ Description: genome assembly-to-assembly comparison
  speed a comparisons of multiple sequences.
  .
  This package is part of the Kmer suite.
+
+Package: kmer-examples
+Architecture: all
+Depends: ${misc:Depends}
+Enhances: sim4db,
+          atac
+Description: sample data for kmer suite of tools for DNA sequence analysis
+ The kmer package is a suite of tools for DNA sequence analysis.
+ It provides tools for searching (ESTs, mRNAs, sequencing reads);
+ aligning (ESTs, mRNAs, whole genomes); and a variety of analyses
+ based on kmers.
+ .
+ This package contains a test data set as well as sample scripts
+ running some test suite provided by Debian also as autopkgtest.

debian/kmer-examples.README.Debian

+This package provides test data for the kmer components atac and sim4db
+_______________________________________________________________________
+
+To test atac run:
+
+	sh /usr/share/doc/atac/atac-unit-test
+
+To test sim4db run:
+
+        sh /usr/share/doc/sim4db/sim4db-unit-test

debian/kmer-examples.docs

+debian/tests/test-data/test_data.tar.gz

debian/sim4db.docs

 README.sim4db
 debian/tests/sim4db-unit-test
-debian/tests/test-data/test_data.tar.gz
 debian/README.test

debian/tests/atac-unit-test

@@ -6,9 +6,19 @@ if [ "$AUTOPKGTEST_TMP" = "" ]; then
     AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
     trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
 fi
+ORIGDIR=`pwd`
 cd $AUTOPKGTEST_TMP
-cp /usr/share/doc/${pkg}/test_data.tar.gz .
-tar -xzvf *.tar.gz; rm *.tar.gz
+if [ -e /usr/share/doc/kmer-examples/test_data.tar.gz ] ; then
+    TARFILE=/usr/share/doc/kmer-examples/test_data.tar.gz
+else
+    if [ -e ${ORIGDIR}/debian/tests/test-data/test_data.tar.gz ] ; then
+        TARFILE=${ORIGDIR}/debian/tests/test-data/test_data.tar.gz
+    else
+        echo "Please install package kmer-examples to run this script"
+        exit 1
+    fi
+fi
+tar -xaf $TARFILE
 
 # Run atac:
 atac -meryldir meryldir -dir results -id1 Lepr -seq1 GCF_000195855.1_ASM19585v1_genomic.fna \

debian/tests/sim4db-unit-test

@@ -6,9 +6,19 @@ if [ "$AUTOPKGTEST_TMP" = "" ]; then
     AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
     trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
 fi
+ORIGDIR=`pwd`
 cd $AUTOPKGTEST_TMP
-cp /usr/share/doc/${pkg}/test_data.tar.gz .
-tar -xzvf *.tar.gz; rm *.tar.gz
+if [ -e /usr/share/doc/kmer-examples/test_data.tar.gz ] ; then
+    TARFILE=/usr/share/doc/kmer-examples/test_data.tar.gz
+else
+    if [ -e ${ORIGDIR}/debian/tests/test-data/test_data.tar.gz ] ; then
+        TARFILE=${ORIGDIR}/debian/tests/test-data/test_data.tar.gz
+    else
+        echo "Please install package kmer-examples to run this script"
+        exit 1
+    fi
+fi
+tar -xaf $TARFILE
 
 # Run sim4db
 echo "Testing sim4 for intra-species alignment...\n"