Andreas Tille pushed to branch master at Debian Med / pirs
Commits: 69fa5d01 by Andreas Tille at 2021-08-31T15:58:41+02:00 routine-update: Fix watchfile to detect new versions on github - - - - - e2ce3eed by Andreas Tille at 2021-08-31T15:59:06+02:00 routine-update: Standards-Version: 4.6.0 - - - - - ec9ca2aa by Andreas Tille at 2021-08-31T15:59:12+02:00 Apply multi-arch hints. + pirs-examples, pirs-profiles: Add Multi-Arch: foreign. Changes-By: apply-multiarch-hints - - - - - 63c63cdb by Andreas Tille at 2021-08-31T16:15:00+02:00 Use default name run-unit-test for autopkgtest script - - - - - 44f20b4c by Andreas Tille at 2021-08-31T16:17:07+02:00 Upload to unstable - - - - - 8 changed files: - + debian/README.test - debian/changelog - debian/control - debian/pirs.docs - debian/tests/control - − debian/tests/gcContCvgBias-test - debian/tests/pirs-test → debian/tests/run-unit-test - debian/watch Changes: ===================================== debian/README.test ===================================== @@ -0,0 +1,9 @@ +Notes on how this package can be tested. +──────────────────────────────────────── + +This package can be tested by running the provided test: + + sudo apt install pirs-examples + sh run-unit-test + +in order to confirm its integrity. ===================================== debian/changelog ===================================== @@ -1,3 +1,13 @@ +pirs (2.0.2+dfsg-10) unstable; urgency=medium + + * Fix watchfile to detect new versions on github (routine-update) + * Standards-Version: 4.6.0 (routine-update) + * Apply multi-arch hints. + + pirs-examples, pirs-profiles: Add Multi-Arch: foreign. + * Use default name run-unit-test for autopkgtest script + + -- Andreas Tille <[email protected]> Tue, 31 Aug 2021 16:15:12 +0200 + pirs (2.0.2+dfsg-9) unstable; urgency=medium * Standards-Version: 4.5.1 (routine-update) ===================================== debian/control ===================================== @@ -7,7 +7,7 @@ Build-Depends: debhelper-compat (= 13), libboost-dev, zlib1g-dev, libgzstream-dev -Standards-Version: 4.5.1 +Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/pirs Vcs-Git: https://salsa.debian.org/med-team/pirs.git Homepage: https://github.com/galaxy001/pirs @@ -42,6 +42,7 @@ Description: Profile based Illumina pair-end Reads Simulator Package: pirs-profiles Architecture: all Depends: ${misc:Depends} +Multi-Arch: foreign Description: profile basd Illumina pair-end Reads Simulator (profile data) The program pIRS can be used for simulating Illumina PE reads, with a series of characters generated by Illumina sequencing platform, such as @@ -66,6 +67,7 @@ Description: profile basd Illumina pair-end Reads Simulator (profile data) Package: pirs-examples Architecture: all Depends: ${misc:Depends} +Multi-Arch: foreign Description: profile basd Illumina pair-end Reads Simulator (example data) The program pIRS can be used for simulating Illumina PE reads, with a series of characters generated by Illumina sequencing platform, such as ===================================== debian/pirs.docs ===================================== @@ -1 +1,3 @@ README +debian/tests/run-unit-test +debian/README.test ===================================== debian/tests/control ===================================== @@ -1,2 +1,3 @@ -Tests: gcContCvgBias-test, pirs-test +Tests: run-unit-test Depends: @, pirs-examples +Restrictions: allow-stderr ===================================== debian/tests/gcContCvgBias-test deleted ===================================== @@ -1,18 +0,0 @@ -#!/bin/sh -e - -pkg=pirs -testbin=gcContCvgBias - -if [ "$AUTOPKGTEST_TMP" = "" ] ; then - AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-${testbin}-test.XXXXXX) - # trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM -fi - -cd $AUTOPKGTEST_TMP - -cp -a /usr/share/doc/${pkg}/examples/${testbin}/* . -# find . -type f -name "*.gz" -exec gunzip \{\} \; -gc_coverage_bias -r gcdeptestref.fa.gz -o test -w 100,200 --gcdump --depwindump gcdeptest.depth.gz -gc_coverage_bias_plot test_100.dat -gc_coverage_bias_plot test_200.dat -ls -l test* ===================================== debian/tests/pirs-test → debian/tests/run-unit-test ===================================== @@ -1,16 +1,28 @@ #!/bin/sh -e pkg=pirs -testbin=pirs if [ "$AUTOPKGTEST_TMP" = "" ] ; then AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-${testbin}-test.XXXXXX) - # trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM + trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM fi cd $AUTOPKGTEST_TMP -cp -a /usr/share/doc/${pkg}/examples/${testbin}/* . +mkdir gcContCvgBias +cd gcContCvgBias +cp -a /usr/share/doc/${pkg}/examples/gcContCvgBias/* . +# find . -type f -name "*.gz" -exec gunzip \{\} \; +gc_coverage_bias -r gcdeptestref.fa.gz -o test -w 100,200 --gcdump --depwindump gcdeptest.depth.gz +gc_coverage_bias_plot test_100.dat +gc_coverage_bias_plot test_200.dat +ls -l test* + +cd .. + +mkdir pirs +cd pirs +cp -a /usr/share/doc/${pkg}/examples/pirs/* . find . -type f -name "*.gz" -exec gunzip \{\} \; pirs diploid ref_seq.fa -s 0.001 -R 2 -d 0.0001 -v 0.000001 -c gzip -o ref22 >SimDiploid.out 2>SimDiploid.err ===================================== debian/watch ===================================== @@ -1,4 +1,4 @@ version=4 opts="uversionmangle=s/b/~b/;s/(\d)(\d+)/$1.$2/,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \ - https://github.com/galaxy001/pirs/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) \ No newline at end of file + https://github.com/galaxy001/pirs/tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/pirs/-/compare/f0503002be355f5cfde1faabd0de51393778246b...44f20b4c5c5036f7e0d0a71b01b1e9c8ab88397f -- View it on GitLab: https://salsa.debian.org/med-team/pirs/-/compare/f0503002be355f5cfde1faabd0de51393778246b...44f20b4c5c5036f7e0d0a71b01b1e9c8ab88397f You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
