[med-svn] [blobology] 02/02: Initial Debian packaging
Andreas Tille
tille at debian.org
Fri Oct 21 10:50:42 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository blobology.
commit f86714b096b176d438a83a28581ccb5a0f3902fe
Author: Andreas Tille <tille at debian.org>
Date: Fri Oct 21 12:49:55 2016 +0200
Initial Debian packaging
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 31 +++++++++++++++++++++++++++++++
debian/copyright | 11 +++++++++++
debian/get-orig-source | 24 ++++++++++++++++++++++++
debian/rules | 26 ++++++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 11 +++++++++++
debian/watch | 4 ++++
9 files changed, 114 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..299a36b
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+blobology (0.0+20151216-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Fri, 21 Oct 2016 12:12:18 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..6ee8ccc
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,31 @@
+Source: blobology
+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 (>= 9)
+Standards-Version: 3.9.8
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/blobology.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/blobology.git
+Homepage: https://blobtools.readme.io/
+
+Package: blobology
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: tool set for the visualisation of genome assemblies
+ Tools for making blobplots or Taxon-Annotated-GC-Coverage plots
+ (TAGC plots) to visualise the contents of genome assembly data sets
+ as a QC step.
+ .
+ blobtools consist of a series of tools that can be used to
+ * collate information associated with an assembly file, such as:
+ - sequence ID
+ - sequence length
+ - GC-content
+ - coverage information
+ - taxonomy information (sequence similarity search hits)
+ - user-defined categories
+ * visualise information using blobplots, covplots and/or readcovplots.
+ * extract information into human- and computer-readable files
+ * produce paper-ready figures
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..de22c77
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,11 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: blobology
+Source: https://github.com/blaxterlab/blobology
+
+Files: *
+Copyright: © 20xx-20yy <upstream>
+License: <license>
+
+Files: debian/*
+Copyright: © 2016 maintainername <maintainer at e.mail>
+License: <license>
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..1a71db8
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,24 @@
+#!/bin/sh -e
+
+COMPRESS=xz
+
+NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+MVERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/^\([0-9\.]\+\)[+~][-0-9]\+$/\1/'`
+
+mkdir -p ../tarballs
+cd ../tarballs
+# need to clean up the tarballs dir first because upstream tarball might
+# contain a directory with unpredictable name
+rm -rf *
+git clone --quiet https://github.com/blaxterlab/blobology
+cd $NAME
+VERSION=${MVERSION}+`date -d @$(git show --format="%at" | head -n1) +%Y%m%d`
+# for esthetical reasons set file timestamps (if git-restore-mtime is installed)
+git restore-mtime || true
+cd ..
+TARDIR=${NAME}-${VERSION}
+mv ${NAME} ${TARDIR}
+rm -rf ${TARDIR}/.git
+
+GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}"
+rm -rf ${TARDIR}
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..1ef14d9
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,26 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+# some helpful variables - uncomment them if needed
+# shamelessly stolen from http://jmtd.net/log/awk/
+#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
+#GIT_TAG := $(subst ~,_,$(VERSION))
+
+# alternatively to manually set those variables, you can
+# include /usr/share/dpkg/default.mk
+# and use what is set there.
+
+# for hardening you might like to uncomment this:
+# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+%:
+ dh $@
+
+#get-orig-source:
+# . debian/get-orig-source
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..5f6e65b
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,11 @@
+Reference:
+ Author: Sujai Kumar and Martin Jones and Georgios Koutsovoulos and Michael Clarke and Mark Blaxter
+ Title: "Blobology: exploring raw genome data for contaminants, symbionts, and parasites using taxon-annotated GC-coverage plots"
+ Journal: frontiers in Genetics
+ Year: 2013
+ Volume: 4
+ Pages: 237
+ DOI: 10.3389/fgene.2013.00237
+ PMID: 24348509
+ URL: http://journal.frontiersin.org/article/10.3389/fgene.2013.00237/full
+ eprint: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3843372/pdf/fgene-04-00237.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..4723d40
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+# no upstream releases
+version=4
+opts=dversionmangle=s/.*/0.No-Release/ \
+https://people.debian.org/~eriberto/ FakeWatchNoUpstreamReleaseForThisPackage-(\d\S+)\.gz
--
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