Andreas Tille pushed to branch master at Debian Med / deepbinner
Commits: c261fa92 by Andreas Tille at 2018-12-17T08:21:21Z Initial packaging - - - - - fa5651fc by Andreas Tille at 2018-12-17T08:25:48Z Add todo list - - - - - 8 changed files: - + debian/changelog - + debian/compat - + debian/control - + debian/copyright - + debian/rules - + debian/source/format - + debian/upstream/metadata - + debian/watch Changes: ===================================== debian/changelog ===================================== @@ -0,0 +1,11 @@ +deepbinner (0.2.0-1) UNRELEASED; urgency=medium + + * Initial release (Closes: #<bug>) + TODO: + 1. python3-tensorflow (see + https://lists.debian.org/debian-science/2018/12/msg00023.html ) + 2. https://github.com/caseman/noise + 3. mappy (https://github.com/lh3/minimap2/tree/master/python) + -> minimap2 is in new + + -- Andreas Tille <[email protected]> Mon, 10 Dec 2018 13:34:46 +0100 ===================================== debian/compat ===================================== @@ -0,0 +1 @@ +11 ===================================== debian/control ===================================== @@ -0,0 +1,48 @@ +Source: deepbinner +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Andreas Tille <[email protected]> +Section: science +Priority: optional +Build-Depends: debhelper (>= 11~), + dh-python, + python3, + python3-setuptools, + python3-keras, + python3-h5py, + python3-numpy, + python3-edlib, +# python3-mappy, +# python3-noise, +# python3-tensorflow +Standards-Version: 4.2.1 +Vcs-Browser: https://salsa.debian.org/med-team/deepbinner +Vcs-Git: https://salsa.debian.org/med-team/deepbinner.git +Homepage: https://github.com/rrwick/Deepbinner + +Package: deepbinner +Architecture: any +Depends: ${shlibs:Depends}, + ${misc:Depends} +Description: demultiplexing barcoded Oxford Nanopore sequencing reads + Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore + sequencing reads. It does this with a deep convolutional neural network + classifier, using many of the architectural advances that have proven + successful in image classification. Unlike other demultiplexers (e.g. + Albacore and Porechop), Deepbinner identifies barcodes from the raw + signal (a.k.a. squiggle) which gives it greater sensitivity and fewer + unclassified reads. + . + Reasons to use Deepbinner: + * To minimise the number of unclassified reads (use Deepbinner + by itself). + * To minimise the number of misclassified reads (use Deepbinner in + conjunction with Albacore demultiplexing). + * You plan on running signal-level downstream analyses, like + Nanopolish. Deepbinner can demultiplex the fast5 files which makes + this easier. Reasons to not use Deepbinner: + * You only have basecalled reads not the raw fast5 files (which + Deepbinner requires). + * You have a small/slow computer. Deepbinner is more computationally + intensive than Porechop. + * You used a sequencing/barcoding kit other than the ones Deepbinner + was trained on. ===================================== debian/copyright ===================================== @@ -0,0 +1,16 @@ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: <pkg> +Source: <path_to_download> +Comment: **** Before manually editing this file you should give **** + scan-copyrights + **** available in cme + lib-config-model-dpkg-perl **** + **** package a try. For existing copyright files try **** + cme update dpkg-copyright + +Files: * +Copyright: © 20xx-20yy <upstream> +License: <license> + +Files: debian/* +Copyright: 2018 Andreas Tille <[email protected]> +License: <license> ===================================== debian/rules ===================================== @@ -0,0 +1,27 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 +export LC_ALL=C.UTF-8 + +include /usr/share/dpkg/default.mk +# this provides: +# DEB_SOURCE: the source package name +# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision) +# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision +# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch +# DEB_VERSION_UPSTREAM: the package's upstream version +# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog +# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as +# specified by <https://reproducible-builds.org/specs/source-date-epoch/> + +# for hardening you might like to uncomment this: +# export DEB_BUILD_MAINT_OPTIONS=hardening=+all + +%: + dh $@ --with python3 --buildsystem=pybuild + +### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected +#override_dh_auto_test: +#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) +# do_stuff_for_testing +#endif ===================================== debian/source/format ===================================== @@ -0,0 +1 @@ +3.0 (quilt) ===================================== debian/upstream/metadata ===================================== @@ -0,0 +1,12 @@ +Reference: + Author: Ryan R Wick and Louise M Judd and Kathryn E Holt + Title: "Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks" + Journal: bioRxiv + Year: 2018 + Volume: 14 + Number: 11 + Pages: e1006583 + DOI: 10.1101/366526 + PMID: 30458005 + URL: https://www.biorxiv.org/content/early/2018/07/10/366526 + eprint: https://www.biorxiv.org/content/biorxiv/early/2018/07/10/366526.full.pdf ===================================== debian/watch ===================================== @@ -0,0 +1,3 @@ +version=4 + +https://github.com/rrwick/Deepbinner/releases .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@ View it on GitLab: https://salsa.debian.org/med-team/deepbinner/compare/e910ed671d00c25df1f241649b890a1454fbc520...fa5651fc6257427b2e75ef36d0bbf0950e3e5dfa -- View it on GitLab: https://salsa.debian.org/med-team/deepbinner/compare/e910ed671d00c25df1f241649b890a1454fbc520...fa5651fc6257427b2e75ef36d0bbf0950e3e5dfa You're receiving this email because of your account on salsa.debian.org.
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