[med-svn] r16639 - in trunk/packages/smalt/trunk/debian: . tests

[Andreas Tille]

Author: tille
Date: 2014-04-09 13:22:32 +0000 (Wed, 09 Apr 2014)
New Revision: 16639

Added:
   trunk/packages/smalt/trunk/debian/smalt-examples.install
   trunk/packages/smalt/trunk/debian/smalt.install
   trunk/packages/smalt/trunk/debian/tests/
   trunk/packages/smalt/trunk/debian/tests/control
   trunk/packages/smalt/trunk/debian/tests/run-unit-test
Modified:
   trunk/packages/smalt/trunk/debian/control
   trunk/packages/smalt/trunk/debian/rules
Log:
Use testsuite as autopkgtest


Modified: trunk/packages/smalt/trunk/debian/control
===================================================================
--- trunk/packages/smalt/trunk/debian/control	2014-04-09 13:18:38 UTC (rev 16638)
+++ trunk/packages/smalt/trunk/debian/control	2014-04-09 13:22:32 UTC (rev 16639)
@@ -1,5 +1,6 @@
 Source: smalt
 Section: science
+XS-Testsuite: autopkgtest
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille at debian.org>
@@ -15,7 +16,7 @@
 Package: smalt
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: efficiently align DNA sequencing reads with a reference genome
+Description: Sequence Mapping and Alignment Tool
  SMALT efficiently aligns DNA sequencing reads with a reference genome.
  It Reads from a wide range of sequencing platforms, for example Illumina,
  Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including
@@ -36,3 +37,30 @@
  .
  A mode for the detection of split (chimeric) reads is provided.
  Multi-threaded program execution is supported.
+
+Package: smalt-examples
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Sequence Mapping and Alignment Tool (examples)
+ SMALT efficiently aligns DNA sequencing reads with a reference genome.
+ It Reads from a wide range of sequencing platforms, for example Illumina,
+ Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including
+ paired reads.
+ .
+ The software employs a perfect hash index of short words (< 20
+ nucleotides long), sampled at equidistant steps along the genomic
+ reference sequences.
+ .
+ For each read, potentially matching segments in the reference are
+ identified from seed matches in the index and subsequently aligned with
+ the read using a banded Smith-Waterman algorithm.
+ .
+ The best gapped alignments of each read is reported including a score
+ for the reliability of the best mapping. The user can adjust the
+ trade-off between sensitivity and speed by tuning the length and spacing
+ of the hashed words.
+ .
+ A mode for the detection of split (chimeric) reads is provided.
+ Multi-threaded program execution is supported.
+ .
+ This package contains example data and a test suite to test the data.

Modified: trunk/packages/smalt/trunk/debian/rules
===================================================================
--- trunk/packages/smalt/trunk/debian/rules	2014-04-09 13:18:38 UTC (rev 16638)
+++ trunk/packages/smalt/trunk/debian/rules	2014-04-09 13:22:32 UTC (rev 16639)
@@ -29,6 +29,13 @@
 override_dh_auto_install:
 	# upstream install does install more files than needed
 
+override_dh_install:
+	dh_install
+	# fix path to smalt executable in examples
+	for py in `ls test/*.py` ; do \
+	    sed 's#PROGNAM = "../src/smalt"#PROGNAM = "/usr/bin/smalt"#' $${py} > debian/smalt-examples/usr/share/doc/smalt/$${py} ; \
+	done
+
 override_dh_auto_clean:
 	dh_auto_clean
 	rm -fr test/*.pyc test/tmp

Added: trunk/packages/smalt/trunk/debian/smalt-examples.install
===================================================================
--- trunk/packages/smalt/trunk/debian/smalt-examples.install	                        (rev 0)
+++ trunk/packages/smalt/trunk/debian/smalt-examples.install	2014-04-09 13:22:32 UTC (rev 16639)
@@ -0,0 +1,2 @@
+test/*.py	usr/share/doc/smalt/test
+test/data	usr/share/doc/smalt/test

Added: trunk/packages/smalt/trunk/debian/smalt.install
===================================================================
--- trunk/packages/smalt/trunk/debian/smalt.install	                        (rev 0)
+++ trunk/packages/smalt/trunk/debian/smalt.install	2014-04-09 13:22:32 UTC (rev 16639)
@@ -0,0 +1,2 @@
+src/smalt				usr/bin
+test/sequenceReverseComplement_test	usr/lib/smalt/test

Added: trunk/packages/smalt/trunk/debian/tests/control
===================================================================
--- trunk/packages/smalt/trunk/debian/tests/control	                        (rev 0)
+++ trunk/packages/smalt/trunk/debian/tests/control	2014-04-09 13:22:32 UTC (rev 16639)
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @builddeps@, smalt-examples
+Restrictions: allow-stderr

Added: trunk/packages/smalt/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/smalt/trunk/debian/tests/run-unit-test	                        (rev 0)
+++ trunk/packages/smalt/trunk/debian/tests/run-unit-test	2014-04-09 13:22:32 UTC (rev 16639)
@@ -0,0 +1,21 @@
+#!/bin/sh -e
+
+if [ "$ADTTMP" = "" ] ; then
+  ADTTMP=`mktemp -d /tmp/smalt-test.XXXXXX`
+fi
+cd $ADTTMP
+cp -a /usr/share/doc/smalt/test/* $ADTTMP
+gunzip *.py.gz
+
+TESTS="splitReads_test.py
+       results_split_test.py
+       ouform_cigar_test.py
+       sample_test.py
+       cigar_test.py
+       mthread_test.py"
+
+ln -s /usr/lib/smalt/test/sequenceReverseComplement_test .
+for tst in $TESTS ; do
+    python $tst
+done
+


Property changes on: trunk/packages/smalt/trunk/debian/tests/run-unit-test
___________________________________________________________________
Added: svn:executable
   + *