[med-svn] [Git][med-team/pairtools][master] Builds and close to lintian-clean
Antoni Villalonga
gitlab at salsa.debian.org
Fri Jun 19 22:16:39 BST 2020
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 <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Antoni Villalonga <antoni at friki.cat>
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 <espresso at mit.edu>
License: MIT
MIT License
.
=====================================
debian/patches/fix-spelling
=====================================
@@ -0,0 +1,28 @@
+Description: Fix spelling errors
+Author: Antoni Villalonga i Noceras <antoni at friki.cat>
+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 <antoni at friki.cat>
+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
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