debian/changelog

+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 <tille@debian.org>  Mon, 10 Dec 2018 13:34:46 +0100

debian/compat

+11

debian/control

+Source: deepbinner
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille@debian.org>
+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

+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 <tille@debian.org>
+License: <license>

debian/rules

+#!/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

+3.0 (quilt)

debian/upstream/metadata

+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

+version=4
+
+https://github.com/rrwick/Deepbinner/releases .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@