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 <[email protected]> Uploaders: Andreas Tille <[email protected]> @@ -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 + * _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
