[med-svn] [roary] 02/07: add debian dir
Sascha Steinbiss
sascha at steinbiss.name
Sun Dec 20 14:17:49 UTC 2015
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository roary.
commit b27d0a61c5f1dce951c135231544b9d67f1d754b
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Thu Dec 17 22:56:27 2015 +0000
add debian dir
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 54 ++++++++++++++++++++++++++++++++++++++++++++++++
debian/copyright | 29 ++++++++++++++++++++++++++
debian/rules | 9 ++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 +++++++++++
debian/watch | 3 +++
8 files changed, 114 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..335d628
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+roary (3.5.7+dfsg-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Thu, 17 Dec 2015 15:36:09 +0000
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..b0cff2a
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,54 @@
+Source: roary
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Sascha Steinbiss <sascha at steinbiss.name>
+Build-Depends: debhelper (>= 9),
+ dh-dist-zilla,
+ libdist-zilla-plugin-podweaver-perl
+Build-Depends-Indep: perl
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/<pkg>/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/<pkg>/trunk/
+Homepage: http://sanger-pathogens.github.io/Roary/
+
+Package: roary
+Architecture: all
+Depends: ${perl:Depends},
+ ${misc:Depends},
+ perl-modules,
+ bioperl,
+ libarray-utils-perl,
+ libenv-path-perl,
+ libexception-class-perl,
+ libfile-find-rule-perl,
+ libfile-slurper-perl,
+ libfile-which-perl,
+ libfindbin-libs-perl,
+ libgraph-perl,
+ libgraph-readwrite-perl,
+ liblog-log4perl-perl,
+ libmoose-perl,
+ libperlio-utf8-strict-perl,
+ libtest-most-perl,
+ libtest-file-perl,
+ libtest-output-perl,
+ libtext-csv-perl,
+ bedtools,
+ cd-hit,
+ ncbi-blast+,
+ mcl,
+ parallel,
+ prank,
+ mafft,
+ fasttree
+Description: high speed stand alone pan genome pipeline
+ Roary is a high speed stand alone pan genome pipeline, which takes annotated
+ assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates
+ the pan genome. Using a standard desktop PC, it can analyse datasets with
+ thousands of samples, something which is computationally infeasible with
+ existing methods, without compromising the quality of the results. 128 samples
+ can be analysed in under 1 hour using 1 GB of RAM and a single processor.
+ To perform this analysis using existing methods would take weeks and hundreds
+ of GB of RAM. Roary is not intended for meta-genomics or for comparing
+ extremely diverse sets of genomes.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..22cc0de
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,29 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Roary
+Source: https://github.com/sanger-pathogens/Roary
+Files-Excluded: binaries contrib
+
+Files: *
+Copyright: © 2014-2015 Genome Research Limited
+License: GPL-3+
+
+Files: debian/*
+Copyright: © 2015 Sascha Steinbiss <sascha at steinbiss.name>
+License: GPL-3+
+
+License: GPL-3+
+ This package 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 package 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.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..90bb740
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+ dh $@ --with dist-zilla
+
+override_dh_auto_test:
+ # pass
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..f39ec1b
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill
+ Title: Roary: Rapid large-scale prokaryote pan genome analysis
+ Journal: Bioinformatics
+ Year: 2015
+ Volume: 31
+ Number: 22
+ Pages: 3691-3693
+ DOI: 10.1093/bioinformatics/btv421
+ PMID: 26198102
+ URL: http://bioinformatics.oxfordjournals.org/content/31/22/3691
+ eprint: http://bioinformatics.oxfordjournals.org/content/31/22/3691.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..b6e401b
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+opts=repacksuffix=+dfsg,dversionmangle=s/\+(debian|dfsg|ds|deb)(\.\d+)?$// \
+https://github.com/sanger-pathogens/roary/tags .*/v?(\d.*)\.(?:tgz|tbz2|txz|tar\.(?:gz|bz2|xz))
--
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