Andreas Tille pushed to branch master at Debian Med / lumpy-sv
Commits: eaa7dcc3 by Andreas Tille at 2020-06-01T22:19:24+02:00 Bamkit is about to be uploaded to new - - - - - dee6e8cf by Andreas Tille at 2020-06-01T23:05:16+02:00 Remove autopkgtest template - - - - - e64a6554 by Andreas Tille at 2020-06-01T23:20:10+02:00 Adapt check to Python3 - - - - - 8 changed files: - − debian/README.test - debian/changelog - debian/control - debian/etc/lumpyexpress.config - debian/install - debian/patches/lumpyexpress.config.patch - − debian/tests/control - − debian/tests/run-unit-test Changes: ===================================== debian/README.test deleted ===================================== @@ -1,8 +0,0 @@ -Notes on how this package can be tested. -──────────────────────────────────────── - -This package can be tested by running the provided test: - - sh run-unit-test - -in order to confirm its integrity. ===================================== debian/changelog ===================================== @@ -1,6 +1,5 @@ -lumpy-sv (0.3.0+dfsg-2) UNRELEASED; urgency=medium +lumpy-sv (0.3.0+dfsg-1) UNRELEASED; urgency=medium * Initial release (Closes: #961998) - TODO: https://salsa.debian.org/med-team/bamkit -- Andreas Tille <[email protected]> Mon, 01 Jun 2020 21:58:38 +0200 ===================================== debian/control ===================================== @@ -27,7 +27,8 @@ Depends: ${shlibs:Depends}, samtools, python3, python3-pysam, - python3-numpy + python3-numpy, + bamkit Recommends: sambamba Description: general probabilistic framework for structural variant discovery LUMPY, a novel SV discovery framework that naturally integrates multiple ===================================== debian/etc/lumpyexpress.config ===================================== @@ -8,6 +8,6 @@ SAMTOOLS=/usr/bin/samtools PYTHON=/usr/bin/python3 PAIREND_DISTRO=/usr/share/lumpy-sv/scripts/pairend_distro.py -#BAMGROUPREADS=/usr/share/lumpy-sv/scripts/bamkit/bamgroupreads.py -#BAMFILTERRG=/usr/share/lumpy-sv/scripts/bamkit/bamfilterrg.py -#BAMLIBS=/usr/share/lumpy-sv/scripts/bamkit/bamlibs.py +BAMGROUPREADS=/usr/share/bamkit/bamgroupreads.py +BAMFILTERRG=/usr/share/bamkit/bamfilterrg.py +BAMLIBS=/usr/share/bamkit/bamlibs.py ===================================== debian/install ===================================== @@ -1,4 +1,4 @@ -debian/etc/lumpyexpress.config etc/lumpy +debian/etc/lumpyexpress.config etc/lumpy-sv scripts usr/share/lumpy-sv bin/lumpy usr/bin bin/lumpy_filter usr/bin ===================================== debian/patches/lumpyexpress.config.patch ===================================== @@ -21,6 +21,17 @@ Description: Adapt paths to Debian locations # For testing if the full BAM is actually a CRAM! HEXDUMP=`which hexdump || true` +@@ -92,8 +92,8 @@ check_python_modules() { + PYTHON_TEST=$1 + echo -e "\nChecking for required python modules ($PYTHON_TEST)..." + +- $PYTHON_TEST -c "import imp; imp.find_module('pysam')" +- $PYTHON_TEST -c "import imp; imp.find_module('numpy')" ++ $PYTHON_TEST -c "import importlib; importlib.util.find_spec('pysam')" ++ $PYTHON_TEST -c "import importlib; importlib.util.find_spec('numpy')" + } + + ## usage @@ -126,7 +126,7 @@ options: # set defaults ===================================== debian/tests/control deleted ===================================== @@ -1,3 +0,0 @@ -Tests: run-unit-test -Depends: @ -Restrictions: allow-stderr ===================================== debian/tests/run-unit-test deleted ===================================== @@ -1,19 +0,0 @@ -#!/bin/bash -set -e - -pkg=#PACKAGENAME# - -export LC_ALL=C.UTF-8 -if [ "${AUTOPKGTEST_TMP}" = "" ] ; then - AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) - # Double quote below to expand the temporary directory variable now versus - # later is on purpose. - # shellcheck disable=SC2064 - trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM -fi - -cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}" - -cd "${AUTOPKGTEST_TMP}" - -#do_stuff_to_test_package# View it on GitLab: https://salsa.debian.org/med-team/lumpy-sv/-/compare/1112e38314b113869a3f4b9748ce484113c9c107...e64a65545fbf60c5c98965bc1d00d416b2f9582c -- View it on GitLab: https://salsa.debian.org/med-team/lumpy-sv/-/compare/1112e38314b113869a3f4b9748ce484113c9c107...e64a65545fbf60c5c98965bc1d00d416b2f9582c You're receiving this email because of your account on salsa.debian.org.
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