[med-svn] [Git][med-team/kmer][master] 2 commits: Provide test data in new package kmer-examples to avoid duplication of data in two packages
Andreas Tille
gitlab at salsa.debian.org
Mon Aug 27 15:51:56 BST 2018
Andreas Tille pushed to branch master at Debian Med / kmer
Commits:
7f2c720d by Andreas Tille at 2018-08-27T14:50:24Z
Provide test data in new package kmer-examples to avoid duplication of data in two packages
- - - - -
1dc82e0f by Andreas Tille at 2018-08-27T14:50:24Z
Upload to unstable
- - - - -
8 changed files:
- debian/atac.docs
- debian/changelog
- debian/control
- + debian/kmer-examples.README.Debian
- + debian/kmer-examples.docs
- debian/sim4db.docs
- debian/tests/atac-unit-test
- debian/tests/sim4db-unit-test
Changes:
=====================================
debian/atac.docs
=====================================
@@ -1,4 +1,3 @@
README.atac
debian/tests/atac-unit-test
-debian/tests/test-data/test_data.tar.gz
debian/README.test
=====================================
debian/changelog
=====================================
@@ -1,11 +1,17 @@
-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 at 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: ${misc:Depends}
+Enhances: sim4db,
+ atac
+Description: sample data for kmer suite of tools for DNA sequence analysis
+ The kmer package is a suite of tools for DNA sequence analysis.
+ It provides tools for searching (ESTs, mRNAs, sequencing reads);
+ aligning (ESTs, mRNAs, whole genomes); and a variety of analyses
+ based on kmers.
+ .
+ This package contains a test data set as well as sample scripts
+ running some test suite provided by Debian also as autopkgtest.
=====================================
debian/kmer-examples.README.Debian
=====================================
@@ -0,0 +1,10 @@
+This package provides test data for the kmer components atac and sim4db
+_______________________________________________________________________
+
+To test atac run:
+
+ sh /usr/share/doc/atac/atac-unit-test
+
+To test sim4db run:
+
+ sh /usr/share/doc/sim4db/sim4db-unit-test
=====================================
debian/kmer-examples.docs
=====================================
@@ -0,0 +1 @@
+debian/tests/test-data/test_data.tar.gz
=====================================
debian/sim4db.docs
=====================================
@@ -1,4 +1,3 @@
README.sim4db
debian/tests/sim4db-unit-test
-debian/tests/test-data/test_data.tar.gz
debian/README.test
=====================================
debian/tests/atac-unit-test
=====================================
@@ -6,9 +6,19 @@ if [ "$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"
View it on GitLab: https://salsa.debian.org/med-team/kmer/compare/2467bacf66b1017368550f041b8b0f638164e256...1dc82e0f62c19816f72ab2e3f62d4efd160f756d
--
View it on GitLab: https://salsa.debian.org/med-team/kmer/compare/2467bacf66b1017368550f041b8b0f638164e256...1dc82e0f62c19816f72ab2e3f62d4efd160f756d
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