Antoni Villalonga pushed to branch master at Debian Med / pairtools
Commits: 385e8109 by Antoni Villalonga at 2020-06-19T23:03:34+02:00 Builds and close to lintian-clean - - - - - 8 changed files: - debian/control - debian/copyright - + debian/patches/fix-spelling - debian/patches/makefile - debian/patches/series - + debian/python3-pairtools.examples - + debian/python3-pairtools.manpages - debian/rules Changes: ===================================== debian/control ===================================== @@ -1,32 +1,60 @@ Source: pairtools -Section: science +Section: python Priority: optional Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Antoni Villalonga <[email protected]> Build-Depends: debhelper-compat (= 13), - python3, dh-python, + python3-all-dev, + python3-all-dbg, + cython3, + cython3-dbg, python3-setuptools, python3-click, python3-numpy, + python3-sphinx-click, Standards-Version: 4.5.0 Homepage: https://github.com/mirnylab/pairtools Vcs-Browser: https://salsa.debian.org/med-team/pairtools Vcs-Git: https://salsa.debian.org/med-team/pairtools.git +Rules-Requires-Root: no Package: python3-pairtools Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends} +Depends: ${shlibs:Depends}, + ${misc:Depends}, + ${python3:Depends}, Description: Framework to process sequencing data from a Hi-C experiment Simple and fast command-line framework to process sequencing data from a Hi-C experiment. . Process pair-end sequence alignments and perform the following operations: . - - Detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end - sequences of Hi-C DNA molecules - - Sort .pairs files for downstream analyses - - Detect, tag and remove PCR/optical duplicates - - Generate extensive statistics of Hi-C datasets - - Select Hi-C pairs given flexibly defined criteria - - Restore .sam alignments from Hi-C pairs + - Detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end + sequences of Hi-C DNA molecules + - Sort .pairs files for downstream analyses + - Detect, tag and remove PCR/optical duplicates + - Generate extensive statistics of Hi-C datasets + - Select Hi-C pairs given flexibly defined criteria + - Restore .sam alignments from Hi-C pairs + +Package: python3-pairtools-dbg +Architecture: any +Section: debug +Depends: ${shlibs:Depends}, + ${misc:Depends}, + ${python3:Depends}, + python3-pairtools (= ${binary:Version}) +Description: Process sequencing data from a Hi-C experiment (debug build) + Debug files for python3-pairtools, a simple and fast command-line framework to + process sequencing data from a Hi-C experiment. + . + Process pair-end sequence alignments and perform the following operations: + . + - Detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end + sequences of Hi-C DNA molecules + - Sort .pairs files for downstream analyses + - Detect, tag and remove PCR/optical duplicates + - Generate extensive statistics of Hi-C datasets + - Select Hi-C pairs given flexibly defined criteria + - Restore .sam alignments from Hi-C pairs ===================================== debian/copyright ===================================== @@ -4,7 +4,7 @@ Upstream-Contact: https://github.com/mirnylab/ Source: https://github.com/mirnylab/pairtools Files: * -Copyright: 2017-2018 Mirny Lab +Copyright: 2017-2018 Mirny Lab <[email protected]> License: MIT MIT License . ===================================== debian/patches/fix-spelling ===================================== @@ -0,0 +1,28 @@ +Description: Fix spelling errors +Author: Antoni Villalonga i Noceras <[email protected]> +Last-Update: Wed, 18 Jun 2020 22:31:00 +0200 + +--- a/doc/parsing.rst ++++ b/doc/parsing.rst +@@ -89,7 +89,7 @@ + ``pairtools parse`` calls an alignment to be multi-mapping when its + `MAPQ score <https://bioinformatics.stackexchange.com/questions/2417/meaning-of-bwa-mem-mapq-scores>`_ + (which depends on the scoring gap between the two best candidate alignments for a segment) +-is equal or greater than the value specied with the ``--min-mapq`` flag (by default, 1). ++is equal or greater than the value specified with the ``--min-mapq`` flag (by default, 1). + + .. _section-walks: + +@@ -124,10 +124,10 @@ + + .. figure:: _static/read_pair_gaps_vs_null_alignment.png + :scale: 50 % +- :alt: A gap between alignments can be ignored or interpeted as a "null" alignment ++ :alt: A gap between alignments can be ignored or interpreted as a "null" alignment + :align: center + +- A gap between alignments can interpeted as a legitimate segment without ++ A gap between alignments can interpreted as a legitimate segment without + an alignment or simply ignored + + Both options have their merits, depending on a dataset, quality of the reference ===================================== debian/patches/makefile ===================================== @@ -1,3 +1,7 @@ +Description: Remove upstream building and publishing script +Author: Antoni Villalonga i Noceras <[email protected]> +Last-Update: Wed, 18 Jun 2020 22:31:00 +0200 + --- a/Makefile +++ /dev/null @@ -1,37 +0,0 @@ ===================================== debian/patches/series ===================================== @@ -1 +1,2 @@ makefile +fix-spelling ===================================== debian/python3-pairtools.examples ===================================== @@ -0,0 +1 @@ +examples/* ===================================== debian/python3-pairtools.manpages ===================================== @@ -0,0 +1 @@ +./doc/_build/man/* ===================================== debian/rules ===================================== @@ -1,11 +1,27 @@ #!/usr/bin/make -f -include /usr/share/dpkg/default.mk +DEB_BUILD_MAINT_OPTIONS = hardening=+all +DPKG_EXPORT_BUILDFLAGS = 1 + +export PYBUILD_DESTDIR_python3=debian/python3-pairtools/ +export PYBUILD_DESTDIR_python3-dbg=debian/python3-pairtools-dbg/ %: dh $@ --with python3 --buildsystem=pybuild override_dh_auto_clean: dh_auto_clean - # for whatever reason cython is called here and leaves unwanted _*.c files behind find . -name "_*.c" -delete + +override_dh_auto_install: + cd doc && make man + dh_auto_install + +override_dh_strip: + dh_strip -ppython3-pairtools --dbg-package=python3-pairtools-dbg + rm -rf debian/python3-pairtools-dbg/usr/share/doc/python3-pairtools-dbg + ln -s python3-pairtools debian/python3-pairtools-dbg/usr/share/doc/python3-pairtools-dbg + +override_dh_installdeb: + rm -rf ./debian/python3-pairtools-dbg/usr/bin + dh_installdeb View it on GitLab: https://salsa.debian.org/med-team/pairtools/-/commit/385e81097ff1c84ebb9767d35cef8c104868bb78 -- View it on GitLab: https://salsa.debian.org/med-team/pairtools/-/commit/385e81097ff1c84ebb9767d35cef8c104868bb78 You're receiving this email because of your account on salsa.debian.org.
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