Author: bob.dybian-guest Date: 2015-01-10 22:48:16 +0000 (Sat, 10 Jan 2015) New Revision: 18562
Added: trunk/packages/plink/trunk/debian/output_tests/ trunk/packages/plink/trunk/debian/output_tests/README trunk/packages/plink/trunk/debian/output_tests/expected.plink.assoc trunk/packages/plink/trunk/debian/output_tests/expected.plink.frq trunk/packages/plink/trunk/debian/tests/ trunk/packages/plink/trunk/debian/tests/control trunk/packages/plink/trunk/debian/tests/run-sample-analysis Modified: trunk/packages/plink/trunk/debian/changelog trunk/packages/plink/trunk/debian/control trunk/packages/plink/trunk/debian/examples Log: Add autopkgtest Modified: trunk/packages/plink/trunk/debian/changelog =================================================================== --- trunk/packages/plink/trunk/debian/changelog 2015-01-10 22:36:51 UTC (rev 18561) +++ trunk/packages/plink/trunk/debian/changelog 2015-01-10 22:48:16 UTC (rev 18562) @@ -7,6 +7,7 @@ [ Dylan Aïssi ] * debian/control: Bump Policy to 3.9.6 (no changes needed) + * Add autopkgtest -- Dylan Aïssi <[email protected]> Sat, 10 Jan 2015 23:30:46 +0100 Modified: trunk/packages/plink/trunk/debian/control =================================================================== --- trunk/packages/plink/trunk/debian/control 2015-01-10 22:36:51 UTC (rev 18561) +++ trunk/packages/plink/trunk/debian/control 2015-01-10 22:48:16 UTC (rev 18562) @@ -7,6 +7,7 @@ Charles Plessy <[email protected]>, Dylan Aïssi <[email protected]> Build-Depends: debhelper (>= 9), zlib1g-dev +Testsuite: autopkgtest Standards-Version: 3.9.6 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/plink/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/plink/trunk/ Modified: trunk/packages/plink/trunk/debian/examples =================================================================== --- trunk/packages/plink/trunk/debian/examples 2015-01-10 22:36:51 UTC (rev 18561) +++ trunk/packages/plink/trunk/debian/examples 2015-01-10 22:48:16 UTC (rev 18562) @@ -1,2 +1,6 @@ +# Upstream samples files test.ped test.map + +# Expected outputs for autopkgtest +debian/output_tests Added: trunk/packages/plink/trunk/debian/output_tests/README =================================================================== --- trunk/packages/plink/trunk/debian/output_tests/README (rev 0) +++ trunk/packages/plink/trunk/debian/output_tests/README 2015-01-10 22:48:16 UTC (rev 18562) @@ -0,0 +1,11 @@ +# Output files (i.e. expected.plink.assoc and expected.plink.frq) were generated following: + +wget http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-1.07-x86_64.zip +unzip plink-1.07-x86_64.zip +cd plink-1.07-x86_64 + +./plink --noweb --file test --freq +mv plink.freq expected.plink.freq + +./plink --noweb --file test --assoc +mv plink.assoc expected.plink.assoc Added: trunk/packages/plink/trunk/debian/output_tests/expected.plink.assoc =================================================================== --- trunk/packages/plink/trunk/debian/output_tests/expected.plink.assoc (rev 0) +++ trunk/packages/plink/trunk/debian/output_tests/expected.plink.assoc 2015-01-10 22:48:16 UTC (rev 18562) @@ -0,0 +1,3 @@ + CHR SNP BP A1 F_A F_U A2 CHISQ P OR + 1 snp1 1 A 0.1667 0.5 C 1.5 0.2207 0.2 + 1 snp2 2 G 0.1667 0.6667 T 3.086 0.07898 0.1 Added: trunk/packages/plink/trunk/debian/output_tests/expected.plink.frq =================================================================== --- trunk/packages/plink/trunk/debian/output_tests/expected.plink.frq (rev 0) +++ trunk/packages/plink/trunk/debian/output_tests/expected.plink.frq 2015-01-10 22:48:16 UTC (rev 18562) @@ -0,0 +1,3 @@ + CHR SNP A1 A2 MAF NCHROBS + 1 snp1 A C 0.3333 12 + 1 snp2 G T 0.4167 12 Added: trunk/packages/plink/trunk/debian/tests/control =================================================================== --- trunk/packages/plink/trunk/debian/tests/control (rev 0) +++ trunk/packages/plink/trunk/debian/tests/control 2015-01-10 22:48:16 UTC (rev 18562) @@ -0,0 +1,2 @@ +Tests: run-sample-analysis +Depends: @ Added: trunk/packages/plink/trunk/debian/tests/run-sample-analysis =================================================================== --- trunk/packages/plink/trunk/debian/tests/run-sample-analysis (rev 0) +++ trunk/packages/plink/trunk/debian/tests/run-sample-analysis 2015-01-10 22:48:16 UTC (rev 18562) @@ -0,0 +1,23 @@ +#!/bin/sh -e +# http://dep.debian.net/deps/dep8/ +# Autopkgtest: Test if plink run analysis correctly +# Author: Dylan Aïssi <[email protected]> +# Last-Update: 2015-01-10 + +pkg=plink +if [ "$ADTTMP" = "" ] ; then + ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` +fi +cd $ADTTMP +cp -a /usr/share/doc/${pkg}/examples/output_tests/* $ADTTMP + +# Allele frequencies +plink --noweb --file test --freq +diff plink.frq expected.plink.frq + +# Case/control or QTL association +plink --noweb --file test --assoc +diff plink.assoc expected.plink.assoc + +rm -f $ADTTMP/* + _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
