Author: tille Date: 2014-04-14 15:58:57 +0000 (Mon, 14 Apr 2014) New Revision: 16702
Added: trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-examples.install trunk/packages/staden-io-lib/trunk/debian/tests/ trunk/packages/staden-io-lib/trunk/debian/tests/control trunk/packages/staden-io-lib/trunk/debian/tests/run-unit-test Modified: trunk/packages/staden-io-lib/trunk/debian/changelog trunk/packages/staden-io-lib/trunk/debian/control trunk/packages/staden-io-lib/trunk/debian/rules Log: use dh-autoreconf; Add autopkgtest using new staden-io-lib-examples package Modified: trunk/packages/staden-io-lib/trunk/debian/changelog =================================================================== --- trunk/packages/staden-io-lib/trunk/debian/changelog 2014-04-14 07:26:28 UTC (rev 16701) +++ trunk/packages/staden-io-lib/trunk/debian/changelog 2014-04-14 15:58:57 UTC (rev 16702) @@ -1,3 +1,12 @@ +staden-io-lib (1.13.5-2) UNRELEASED; urgency=medium + + * use dh-autoreconf + Closes: 744664 + * Add autopkgtest using new staden-io-lib-examples package + + + -- Andreas Tille <[email protected]> Mon, 14 Apr 2014 13:08:48 +0200 + staden-io-lib (1.13.5-1.1) unstable; urgency=medium * Non-maintainer upload. Modified: trunk/packages/staden-io-lib/trunk/debian/control =================================================================== --- trunk/packages/staden-io-lib/trunk/debian/control 2014-04-14 07:26:28 UTC (rev 16701) +++ trunk/packages/staden-io-lib/trunk/debian/control 2014-04-14 15:58:57 UTC (rev 16702) @@ -4,9 +4,10 @@ Andreas Tille <[email protected]>, Thorsten Alteholz <[email protected]> Section: science +XS-Testsuite: autopkgtest Priority: optional Build-Depends: debhelper (>= 9), - autotools-dev, + dh-autoreconf, zlib1g-dev, libcurl4-gnutls-dev | libcurl4-nss-dev, d-shlibs @@ -58,3 +59,20 @@ code to provide a general purpose trace file (and Experiment File) reading interface. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows. + +Package: staden-io-lib-examples +Architecture: all +Depends: ${shlibs:Depends}, + ${misc:Depends} +Description: programs for maniuplating DNA sequencing files + The io_lib from the Staden package is a library of file reading and writing + code to provide a general purpose trace file (and Experiment File) reading + interface. It has been compiled and tested on a variety of unix systems, + MacOS X and MS Windows. + . + This package contains the programs that are distributed with the Staden io_lib + for manipulating and converting sequencing data files, and in particular files + to maniuplate short reads generated by second and third generation sequencers + and stored in SRF format. + . + This package contains example data and a test suite to test the data. Modified: trunk/packages/staden-io-lib/trunk/debian/rules =================================================================== --- trunk/packages/staden-io-lib/trunk/debian/rules 2014-04-14 07:26:28 UTC (rev 16701) +++ trunk/packages/staden-io-lib/trunk/debian/rules 2014-04-14 15:58:57 UTC (rev 16702) @@ -3,11 +3,12 @@ libpkg=libstaden-read devpkg=$(libpkg)-dev #version=$(shell dpkg-parsechangelog -ldebian/changelog | grep Version: | cut -f2 -d' ' | cut -f1 -d- ) -#utils=staden-io-lib-utils +srcname=staden-io-lib +testdir=debian/$(srcname)-examples/usr/share/doc/$(srcname)/test #mandir=$(CURDIR)/debian/$(utils)/usr/share/man/man1/ %: - dh $@ --with autotools_dev + dh $@ --with autoreconf override_dh_install: dh_install @@ -30,7 +31,18 @@ # --name='filter SRF files for various purposes' \ # --version-string="$(version)" \ # $(CURDIR)/debian/$(utils)/usr/bin/srf_filter > $(mandir)/srf_filter.1 + mkdir -p $(testdir) + # fix path to staden-io-lib executable in examples + for tst in `ls tests/*.test` ; do \ + sed 's#$$top_builddir/progs/#/usr/bin/#' $${tst} > $(testdir)/`basename $${tst}` ; \ + done + # remove autogenerated big data files + rm -f $(testdir)/data/ce\#*sorted.sam +override_dh_fixperms: + dh_fixperms + chmod +x $(testdir)/*.test $(testdir)/*.pl + override_dh_auto_clean: dh_auto_clean rm -f tests/.done tests/data/ce\#sorted.sam tests/data/ce\#unsorted.sam Added: trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-examples.install =================================================================== --- trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-examples.install (rev 0) +++ trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-examples.install 2014-04-14 15:58:57 UTC (rev 16702) @@ -0,0 +1,2 @@ +tests/*.pl usr/share/doc/staden-io-lib/test +tests/data usr/share/doc/staden-io-lib/test Added: trunk/packages/staden-io-lib/trunk/debian/tests/control =================================================================== --- trunk/packages/staden-io-lib/trunk/debian/tests/control (rev 0) +++ trunk/packages/staden-io-lib/trunk/debian/tests/control 2014-04-14 15:58:57 UTC (rev 16702) @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @, staden-io-lib-utils, smalt-examples +Restrictions: allow-stderr Added: trunk/packages/staden-io-lib/trunk/debian/tests/run-unit-test =================================================================== --- trunk/packages/staden-io-lib/trunk/debian/tests/run-unit-test (rev 0) +++ trunk/packages/staden-io-lib/trunk/debian/tests/run-unit-test 2014-04-14 15:58:57 UTC (rev 16702) @@ -0,0 +1,18 @@ +#!/bin/sh -e + +if [ "$ADTTMP" = "" ] ; then + ADTTMP=`mktemp -d /tmp/staden-io-lib-test.XXXXXX` +fi +cd $ADTTMP +cp -a /usr/share/doc/staden-io-lib/test/* $ADTTMP +gunzip data/*.gz + +TESTS=`ls *.test` +OUTDIR=./test.out +LOGFILE=`basename $0`.log + +mkdir -p $OUTDIR +for tst in $TESTS ; do + srcdir=. outdir=$OUTDIR $tst > $LOGFILE +done + Property changes on: trunk/packages/staden-io-lib/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
