[med-svn] [tn-seqexplorer] 02/02: initial packaging
Andreas Tille
tille at debian.org
Fri May 5 19:22:56 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository tn-seqexplorer.
commit 1c550a1a1f0e250314d4d17b1feed35ec36e9e63
Author: Andreas Tille <tille at debian.org>
Date: Fri May 5 21:13:57 2017 +0200
initial packaging
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 31 +++++++++++++++++++++++++++++++
debian/copyright | 16 ++++++++++++++++
debian/get-orig-source | 28 ++++++++++++++++++++++++++++
debian/rules | 25 +++++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++++++++++
debian/watch | 6 ++++++
9 files changed, 125 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..eb34658
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+tn-seqexplorer (0.0+20151207-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Fri, 05 May 2017 15:37:33 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..116ba51
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,31 @@
+Source: tn-seqexplorer
+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 (>= 10),
+ javahelper,
+ default-jdk,
+ libcommons-io-java,
+ libcommons-math-java,
+ libcommons-math-java-doc,
+ libcommons-net-java (>= 3.3),
+ libguava-java,
+ libjcommon-java,
+ libjfreechart-java (>= 1.0.16),
+ liblog4j1.2-java
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/tn-seqexplorer.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/tn-seqexplorer.git
+Homepage: https://github.com/sina-cb/Tn-seqExplorer
+
+Package: tn-seqexplorer
+Architecture: all
+Depends: ${java:Depends},
+ ${misc:Depends}
+Description: explore and analyze Tn-seq data for prokaryotic genomes
+ Tn-seq Explorer allows users to explore and analyze Tn-seq data for
+ prokaryotic (bacterial or archaeal) genomes. It implements two
+ alternative methods for identification of essential genes and provides
+ additional tools to investigate the Tn-seq data. The primary goal of the
+ data analysis is to study fitness by identifying genes that are essentia
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..c8c6bef
--- /dev/null
+++ b/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: 2017 Andreas Tille <tille at debian.org>
+License: <license>
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..ab2dc0c
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,28 @@
+#!/bin/sh -e
+
+COMPRESS=xz
+
+NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+ONAME=Tn-seqExplorer
+MVERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/^\([0-9\.]\+\)[+~][-0-9]\+$/\1/'`
+
+mkdir -p ../tarballs
+cd ../tarballs
+# need to clean up the tarballs dir first because upstream tarball might
+# contain a directory with unpredictable name
+rm -rf *
+git clone --quiet https://github.com/sina-cb/${ONAME} ${NAME}
+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
+find ${TARDIR} -name .DS_Store -delete
+find ${TARDIR} -name *.jar -delete
+find ${TARDIR} -name *.zip -delete
+
+GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}"
+rm -rf ${TARDIR}
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..3cdbf28
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,25 @@
+#!/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))
+
+DEBJAR := /usr/share/java
+CLASS_PATH := $(DEBJAR)/commons-io.jar:$(DEBJAR)/commons-math.jar:$(DEBJAR)/commons-net.jar:$(DEBJAR)/guava.jar:$(DEBJAR)/jcommon.jar:$(DEBJAR)/jfreechart.jar:$(DEBJAR)/log4j-1.2.jar
+
+%:
+ dh $@ --with javahelper
+
+override_dh_auto_build:
+ CLASSPATH=$(CLASS_PATH) jh_build --javacopts='-target 1.7' --javacopts='-source 1.7' $(DEBPKGNAME).jar src
+
+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..2e7ae0c
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Sina Solaimanpour and Felipe Sarmiento and Jan Mrázek
+ Title: "Tn-Seq Explorer: A Tool for Analysis of High-Throughput Sequencing Data of Transposon Mutant Libraries"
+ Journal: PLoS ONE
+ Year: 2015
+ Volume: 10
+ Number: 5
+ Pages: e0126070
+ DOI: 10.1371/journal.pone.0126070
+ PMID: 25938432
+ URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126070
+ eprint: http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0126070&type=printable
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..ad9195c
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,6 @@
+version=4
+
+opts=dversionmangle=s/.*/0.No-Release/ \
+ https://people.debian.org/~eriberto/ FakeWatchNoUpstreamReleaseForThisPackage-(\d\S+)\.gz
+
+# https://github.com/sina-cb/Tn-seqExplorer/issues/2
--
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