[med-svn] [scoary] 02/02: Initial packaging
Afif Elghraoui
afif at moszumanska.debian.org
Mon Jan 16 01:06:07 UTC 2017
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository scoary.
commit f44142cbd8c5d2ac4065472944c6235b1ba98a88
Author: Afif Elghraoui <afif at debian.org>
Date: Sun Jan 15 17:05:53 2017 -0800
Initial packaging
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 30 ++++++++++++++++++++++++++++++
debian/copyright | 27 +++++++++++++++++++++++++++
debian/desktop/scoary.desktop | 12 ++++++++++++
debian/docs | 1 +
debian/install | 1 +
debian/manpages | 1 +
debian/rules | 7 +++++++
debian/scoary.1 | 20 ++++++++++++++++++++
debian/source/format | 1 +
debian/tests/control | 1 +
debian/upstream/metadata | 9 +++++++++
debian/watch | 5 +++++
14 files changed, 121 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..bc23051
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+scoary (1.6.9-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #nnnn)
+
+ -- Afif Elghraoui <afif at debian.org> Sun, 15 Jan 2017 15:16:03 -0800
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..3822f63
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,30 @@
+Source: scoary
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Afif Elghraoui <afif at debian.org>
+Build-Depends:
+ debhelper (>=9),
+ dh-python,
+ python-all,
+ python-setuptools,
+ python-scipy (>= 0.16),
+# Test-Depends:
+ python-nose,
+Standards-Version: 3.9.8
+Homepage: https://github.com/AdmiralenOla/Scoary
+Vcs-Git: https://anonscm.debian.org/debian-med/scoary.git
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/scoary.git
+
+Package: scoary
+Architecture: all
+Depends:
+ ${misc:Depends},
+ ${python:Depends},
+ python-pkg-resources,
+Suggests: roary
+Description: pangenome-wide association studies
+ Scoary is designed to take the gene_presence_absence.csv file from
+ Roary as well as a traits file created by the user and calculate the
+ associations between all genes in the accessory genome and the traits. It
+ reports a list of genes sorted by strength of association per trait.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..cb3ae1d
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,27 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Scoary
+Source: https://github.com/AdmiralenOla/Scoary
+
+Files: *
+Copyright: 2016-2017 Ola Brynildsrud <ola.brynildsrud at fhi.no>
+License: GPL-3.0
+
+Files: debian/*
+Copyright: 2017 Afif Elghraoui <afif at debian.org>
+License: GPL-3.0
+
+License: GPL-3.0
+ 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.
+ .
+ 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 <https://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/desktop/scoary.desktop b/debian/desktop/scoary.desktop
new file mode 100644
index 0000000..38d326a
--- /dev/null
+++ b/debian/desktop/scoary.desktop
@@ -0,0 +1,12 @@
+[Desktop Entry]
+Comment=Pangenome-wide association studies
+Exec=scoary_GUI
+GenericName[en_US]=Scoary
+GenericName=Scoary
+Name[en_US]=Scoary
+Name=Scoary
+Categories=Science;Biology;DataVisualization;
+StartupNotify=false
+Terminal=false
+Type=Application
+Keywords=genomics
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..6339bec
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+debian/desktop/* usr/share/applications/
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..f227160
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/scoary.1
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..872142f
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,7 @@
+#!/usr/bin/make -f
+
+#export DH_VERBOSE = 1
+export LC_ALL = C.UTF-8
+
+%:
+ dh $@ --with python2 --buildsystem=pybuild
diff --git a/debian/scoary.1 b/debian/scoary.1
new file mode 100644
index 0000000..f7459b3
--- /dev/null
+++ b/debian/scoary.1
@@ -0,0 +1,20 @@
+.TH SCOARY 1 "January 2017"
+.SH NAME
+scoary \- pangenome\-wide association studies
+.SH SYNOPSIS
+.B scoary
+.RI [ options ] " files" ...
+.SH DESCRIPTION
+\fBscoary\fP is designed to take the gene_presence_absence.csv file from
+.BR roary (1)
+as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome and the traits.
+It reports a list of genes sorted by strength of association per trait.
+.SH OPTIONS
+For a complete usage description, see the help menu.
+.TP
+.B \-h, \-\-help
+Show summary of options.
+.SH SEE ALSO
+.BR roary (1)
+.br
+/usr/share/doc/scoary/README.md.gz
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/tests/control b/debian/tests/control
new file mode 100644
index 0000000..220a861
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1 @@
+Test-Command: cd $ADTTMP && scoary --test
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..23eceea
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,9 @@
+Reference:
+ Author: Ola Brynildsrud and Jon Bohlin and Lonneke Scheffer and Vegard Eldholm
+ Title: Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary
+ Journal: Genome Biology
+ Year: 2016
+ Volume: 17
+ Number: 238
+ DOI: 10.1186/s13059-016-1108-8
+ URL: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1108-8
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..da7ee90
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,5 @@
+version=4
+
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%scoary-$1.tar.gz%" \
+ https://github.com/AdmiralenOla/Scoary/tags \
+ (?:.*?/)?v?(\d[\d.]*)\.tar\.gz debian uupdate
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