[med-svn] [Git][med-team/deepbinner][master] 2 commits: Initial packaging
Andreas Tille
gitlab at salsa.debian.org
Mon Dec 17 08:26:04 GMT 2018
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 <tille at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at 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
=====================================
@@ -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 <tille at debian.org>
+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
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