[med-svn] [bio-tradis] 02/02: Initial packaging
Andreas Tille
tille at debian.org
Fri Mar 3 22:45:56 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository bio-tradis.
commit dd640f3624d66b92389710f230797d1f8297b93f
Author: Andreas Tille <tille at debian.org>
Date: Fri Mar 3 23:45:15 2017 +0100
Initial packaging
---
debian/README.Debian | 8 ++++++++
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 30 ++++++++++++++++++++++++++++++
debian/copyright | 26 ++++++++++++++++++++++++++
debian/docs | 1 +
debian/install | 2 ++
debian/rules | 11 +++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++++++++++
debian/watch | 4 ++++
11 files changed, 101 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..70b572e
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,8 @@
+Bio-Tradis for Debian
+=====================
+
+Since the PDF documentation is considered as binary without source
+it has to be excluded from the package source. You can find the
+documentation here:
+
+ https://github.com/sanger-pathogens/Bio-Tradis/blob/master/BioTraDISTutorial.pdf
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..e93df53
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+bio-tradis (1.3.1+dfsg-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Fri, 03 Mar 2017 23:01:03 +0100
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..7084b71
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,30 @@
+Source: bio-tradis
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: perl
+Testsuite: autopkgtest-pkg-perl
+Priority: optional
+Build-Depends: debhelper (>= 10)
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bio-tradis.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/bio-tradis.git
+Homepage: https://github.com/sanger-pathogens/Bio-Tradis
+
+Package: bio-tradis
+Architecture: any
+Depends: ${perl:Depends},
+ ${misc:Depends},
+ smalt,
+ samtools,
+ tabix,
+ r-base-core,
+ r-bioc-edger,
+ r-cran-getopt,
+ r-cran-mass
+Description: analyse the output from TraDIS analyses of genomic sequences
+ Bio-Tradis contains a set of tools to analyse the output from
+ TraDIS analyses.
+ .
+ The Bio-Tradis analysis pipeline is implemented as an extensible Perl
+ library which can either be used as is, or as a basis for the
+ development of more advanced analysis tools.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..021738b
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,26 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Bio-Tradis
+Source: https://github.com/sanger-pathogens/Bio-Tradis/releases
+Files-Excluded: BioTraDISTutorial.pdf
+
+Files: *
+Copyright: 2013-2017 Wellcome Trust Sanger Institute
+License: GPL-3+
+
+Files: debian/*
+Copyright: 2017 Andreas Tille <tille at debian.org>
+License: GPL-3+
+
+License: GPL-3+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ On Debian systems you can find the full text of the GNU General Public
+ License at /usr/share/common-licenses/GPL-3.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..b43bf86
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+README.md
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..91ffe16
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,2 @@
+lib/Bio usr/share/perl5
+bin usr
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..1f6f27b
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,11 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+%:
+ dh $@
+
+override_dh_install:
+ dh_install
+ find debian/*/usr/bin -name "*.R" -exec sh -c 'mv {} `echo {} | sed "s/\.R$$//"`' \;
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..cb9e444
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Lars Barquist and Matthew Mayho and Carla Cummins and Amy K. Cain and Christine J. Boinett and Andrew J. Page and Gemma C. Langridge and Michael A. Quail and Jacqueline A. Keane and Julian Parkhill
+ Title: "The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries"
+ Journal: Bioinformatics
+ Year: 2016
+ Volume: 32
+ Number: 7
+ Pages: 1109-1111
+ DOI: 10.1093/bioinformatics/btw022
+ PMID: 26794317
+ URL: https://academic.oup.com/bioinformatics/article/32/7/1109/1744349/The-TraDIS-toolkit-sequencing-and-analysis-for
+ eprint: https://academic.oup.com/bioinformatics/article-pdf/32/7/1109/10764329/btw022.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..5b54e6a
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=4
+
+opts="uversionmangle=s/^1.1/1.1./,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+ https://github.com/sanger-pathogens/Bio-Tradis/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
--
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