Package list python-pauvre / 7aac220
Initial packaging Andreas Tille 2 years ago
11 changed file(s) with 159 addition(s) and 0 deletion(s). Raw diff Collapse all Expand all
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debian/README.test less more
0 Notes on how this package can be tested.
1 ────────────────────────────────────────
2
3 This package can be tested by running the provided test:
4
5 sh run-unit-test
6
7 in order to confirm its integrity.
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debian/changelog less more
0 python-pauvre (0.1924-1) UNRELEASED; urgency=medium
1
2 * Initial release (Closes: #<bug>)
3
4 -- Andreas Tille <tille@debian.org> Fri, 24 Apr 2020 12:49:17 +0200
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debian/control less more
0 Source: python-pauvre
1 Section: science
2 Priority: optional
3 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
4 Uploaders: Andreas Tille <tille@debian.org>
5 Build-Depends: debhelper-compat (= 12),
6 dh-python,
7 python3,
8 python3-setuptools,
9 Standards-Version: 4.5.0
10 Vcs-Browser: https://salsa.debian.org/med-team/python-pauvre
11 Vcs-Git: https://salsa.debian.org/med-team/python-pauvre.git
12 Homepage: https://github.com/conchoecia/pauvre
13
14 Package: python3-pauvre
15 Architecture: all
16 Section: python
17 Depends: ${python3:Depends},
18 ${misc:Depends},
19 python3-matplotlib,
20 python3-biopython,
21 python3-pandas,
22 python3-numpy,
23 python3-scipy,
24 python3-sklearn
25 Description: QC and genome browser plotting Oxford Nanopore and PacBio long reads
26 Pauvre is a plotting package designed for nanopore and PacBio long reads.
27 .
28 This package currently hosts four scripts for plotting and/or printing stats.
29 .
30 pauvre marginplot
31 Takes a fastq file as input and outputs a marginal histogram with a
32 heatmap.
33 pauvre stats
34 Takes a fastq file as input and prints out a table of stats, including
35 how many basepairs/reads there are for a length/mean quality cutoff.
36 This is also automagically called when using pauvre marginplot
37 pauvre redwood
38 Method of representing circular genomes. A redwood plot contains long
39 reads as "rings" on the inside, a gene annotation "cambrium/phloem",
40 and a RNAseq "bark". The input is .bam files for the long reads and
41 RNAseq data, and a .gff file for the annotation.
42 pauvre synteny
43 Makes a synteny plot of circular genomes. Finds the most parsimonius
44 rotation to display the synteny of all the input genomes with the
45 fewest crossings-over. Input is one .gff file per circular genome
46 and one directory of gene alignments.
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debian/copyright less more
0 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
1 Upstream-Name: pauvre
2 Source: https://pypi.org/project/pauvre/#files
3
4 Files: *
5 Copyright: 2016-2020 Darrin T. Schultz
6 License: GPL-3+
7
8 Files: debian/*
9 Copyright: 2020 Andreas Tille <tille@debian.org>
10 License: GPL-3+
11
12 License: GPL-3+
13 pauvre is free software: you can redistribute it and/or modify
14 it under the terms of the GNU General Public License as published by
15 the Free Software Foundation, either version 3 of the License, or
16 (at your option) any later version.
17 .
18 pauvre is distributed in the hope that it will be useful,
19 but WITHOUT ANY WARRANTY; without even the implied warranty of
20 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21 GNU General Public License for more details.
22 .
23 On Debian systems you can find the full text of the GNU General Public
24 License version 3 at /usr/share/common-licenses/GPL-3.
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debian/rules less more
0 #!/usr/bin/make -f
1
2 # DH_VERBOSE := 1
3 export LC_ALL=C.UTF-8
4
5 include /usr/share/dpkg/default.mk
6 # this provides:
7 # DEB_SOURCE: the source package name
8 # DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
9 # DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
10 # DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
11 # DEB_VERSION_UPSTREAM: the package's upstream version
12 # DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
13 # SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as
14 # specified by <https://reproducible-builds.org/specs/source-date-epoch/>
15
16 # for hardening you might like to uncomment this:
17 # export DEB_BUILD_MAINT_OPTIONS=hardening=+all
18
19 %:
20 dh $@ --with python3 --buildsystem=pybuild
21
22 ### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
23 #override_dh_auto_test:
24 #ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
25 # do_stuff_for_testing
26 #endif
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debian/salsa-ci.yml less more
0 ---
1 include:
2 - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
3 - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
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debian/source/format less more
0 3.0 (quilt)
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debian/tests/control less more
0 Tests: run-unit-test
1 Depends: @
2 Restrictions: allow-stderr
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debian/tests/run-unit-test less more
0 #!/bin/bash
1 set -e
2
3 pkg=#PACKAGENAME#
4
5 export LC_ALL=C.UTF-8
6 if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
7 AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
8 # Double quote below to expand the temporary directory variable now versus
9 # later is on purpose.
10 # shellcheck disable=SC2064
11 trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
12 fi
13
14 cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
15
16 cd "${AUTOPKGTEST_TMP}"
17
18 #do_stuff_to_test_package#
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debian/upstream/metadata less more
0 Reference:
1 Author:
2 Title:
3 Journal:
4 Year:
5 Volume:
6 Number:
7 Pages:
8 DOI:
9 PMID:
10 URL:
11 eprint:
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debian/watch less more
0 version=4
1
2 https://pypi.python.org/simple/pauvre .*/pauvre-@ANY_VERSION@@ARCHIVE_EXT@#sha256=.*
3
4 # No tags on Github
5 # see https://github.com/conchoecia/pauvre/issues/38
6 #opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%" \
7 #https://github.com/conchoecia/pauvre/releases .*/archive/v?@ANY_VERSION@\.tar\.gz