Andreas Tille pushed to branch master at Debian Med / python-pairix
Commits: a77b2ba9 by Andreas Tille at 2020-06-14T00:29:19+02:00 try autopkgtest - - - - - 5 changed files: - debian/control - + debian/python3-pairix-examples.install - debian/rules - debian/tests/control - debian/tests/run-unit-test Changes: ===================================== debian/control ===================================== @@ -16,6 +16,7 @@ Homepage: https://github.com/4dn-dcic/pairix Package: python3-pairix Architecture: any +Section: python Depends: ${shlib:Depends}, ${python3:Depends}, ${misc:Depends} @@ -36,3 +37,27 @@ Description: 1D/2D indexing and querying with a pair of genomic coordinates read the Pairs file from beginning to end. Pairix creates an index and uses it to access the file from a relevant position by taking advantage of bgzf compression, allowing for a fast query on large files. + +Package: python3-pairix-examples +Architecture: all +Depends: ${misc:Depends} +Enhances: python3-pairix +Description: 1D/2D indexing and querying with a pair of genomic coordinates (examples) + Pairix is a tool for indexing and querying on a block-compressed text + file containing pairs of genomic coordinates. + . + Pairix is a stand-alone C program that was written on top of tabix as a + tool for the 4DN-standard pairs file format describing Hi-C data: + pairs_format_specification.md + . + However, Pairix can be used as a generic tool for indexing and querying + any bgzipped text file containing genomic coordinates, for either 2D- or + 1D- indexing and querying. + . + For example: given the custom text file below, you want to extract + specific lines from the Pairs file further below. An awk command would + read the Pairs file from beginning to end. Pairix creates an index and + uses it to access the file from a relevant position by taking advantage + of bgzf compression, allowing for a fast query on large files. + . + This package contains some example data to test the package. ===================================== debian/python3-pairix-examples.install ===================================== @@ -0,0 +1 @@ +test usr/share/doc/python2-pairix/examples ===================================== debian/rules ===================================== @@ -4,5 +4,13 @@ export PYBUILD_NAME=pairix +export PYBUILD_BEFORE_TEST=cp -a $(CURDIR)/samples {build_dir}; cp -a $(CURDIR)/VERSION.txt {build_dir}; + %: dh $@ --with python3 --buildsystem=pybuild + +override_dh_installexamples: + dh_installexamples + mkdir -p debian/python3-$(PYBUILD_NAME)-examples/usr/share/doc/python3-$(PYBUILD_NAME)/examples + mv debian/python3-$(PYBUILD_NAME)/usr/lib/python3*/dist-packages/samples debian/python3-$(PYBUILD_NAME)-examples/usr/share/doc/python3-$(PYBUILD_NAME)/examples + mv debian/python3-$(PYBUILD_NAME)/usr/lib/python3*/dist-packages/VERSION.txt debian/python3-$(PYBUILD_NAME)-examples/usr/share/doc/python3-$(PYBUILD_NAME)/examples ===================================== debian/tests/control ===================================== @@ -1,3 +1,3 @@ Tests: run-unit-test -Depends: @ +Depends: @, python3-pytest Restrictions: allow-stderr ===================================== debian/tests/run-unit-test ===================================== @@ -1,7 +1,7 @@ #!/bin/bash set -e -pkg=#PACKAGENAME# +pkg=python3-pairix export LC_ALL=C.UTF-8 if [ "${AUTOPKGTEST_TMP}" = "" ] ; then @@ -16,4 +16,4 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}" cd "${AUTOPKGTEST_TMP}" -#do_stuff_to_test_package# +pytest-3 View it on GitLab: https://salsa.debian.org/med-team/python-pairix/-/commit/a77b2ba9c3d289a3cbddc456ce6763f766b09f37 -- View it on GitLab: https://salsa.debian.org/med-team/python-pairix/-/commit/a77b2ba9c3d289a3cbddc456ce6763f766b09f37 You're receiving this email because of your account on salsa.debian.org.
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