[med-svn] [mapdamage] 02/02: Add initial debian/ dir
Andreas Tille
tille at debian.org
Fri Jul 29 12:46:36 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository mapdamage.
commit 02da13c4b09c1d1b55a8006ab2b879aec8d380af
Author: Andreas Tille <tille at debian.org>
Date: Fri Jul 29 14:46:01 2016 +0200
Add initial debian/ dir
---
debian/changelog | 5 +++
debian/clean | 1 +
debian/compat | 1 +
debian/control | 25 +++++++++++++
debian/copyright | 32 +++++++++++++++++
debian/patches/series | 1 +
debian/patches/use_debian_packaged_seqtk.patch | 50 ++++++++++++++++++++++++++
debian/rules | 6 ++++
debian/source/format | 1 +
debian/upstream/metadata | 12 +++++++
debian/watch | 4 +++
11 files changed, 138 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..69d53d7
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+mapdamage (2.0.6+dfsg-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Thu, 28 Jul 2016 15:13:14 +0200
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..daa30a3
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1 @@
+README.html
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..c883ea9
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,25 @@
+Source: mapdamage
+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),
+ python-all,
+ dh-python,
+ python-setuptools
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/mapdamage.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/mapdamage.git
+Homepage: https://ginolhac.github.io/mapDamage/
+
+Package: mapdamage
+Architecture: all
+Depends: ${python:Depends},
+ ${misc:Depends}
+Description: tracking and quantifying damage patterns in ancient DNA sequences
+ MapDamage is a computational framework written in Python and R, which
+ tracks and quantifies DNA damage patterns among ancient DNA sequencing
+ reads generated by Next-Generation Sequencing platforms.
+ .
+ MapDamage is developed at the Centre for GeoGenetics by the
+ Orlando Group.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..f3fb104
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,32 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: mapDamage
+Source: https://github.com/ginolhac/mapDamage/releases
+Files-Excluded: */seqtk
+ */.gitignore
+
+Files: *
+Copyright: 2012-2015 Jónsson H, Ginolhac A, Schubert M, Johnson P, Orlando L.
+License: expat
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <tille at debian.org>
+License: expat
+
+License: expat
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in all
+ copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..8ac87a5
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+use_debian_packaged_seqtk.patch
diff --git a/debian/patches/use_debian_packaged_seqtk.patch b/debian/patches/use_debian_packaged_seqtk.patch
new file mode 100644
index 0000000..38a37ba
--- /dev/null
+++ b/debian/patches/use_debian_packaged_seqtk.patch
@@ -0,0 +1,50 @@
+--- a/setup.py
++++ b/setup.py
+@@ -6,21 +6,6 @@ from distutils.command.install import in
+ import os
+ import subprocess
+
+-def compile_seqtk():
+- """Compiling the seqtk toolkit"""
+- old_wd = os.getcwd()
+- new_wd = os.path.join(old_wd,"mapdamage","seqtk")
+- os.chdir(new_wd)
+- if not os.path.isfile("seqtk.c"):
+- raise SystemExit("Cannot find seqtk.c")
+- if (os.path.isfile("seqtk")):
+- os.system("rm seqtk")
+- xs = os.system("make -f Makefile")
+- os.chdir(old_wd)
+- if (xs != 0):
+- raise SystemExit("Cannot compile seqtk")
+-
+-
+ def setup_version():
+ if not os.path.exists(".git"):
+ # Release version, no .git folder
+@@ -40,16 +25,7 @@ class compileInstall(DistutilsInstall):
+ def run(self):
+ self.record=""
+ setup_version()
+- compile_seqtk()
+ DistutilsInstall.run(self)
+- # fixing the permission problem of seqtk
+- files = self.get_outputs()
+- for fi in files:
+- if fi.endswith("seqtk/seqtk"):
+- os.chmod(fi,0755)
+-
+-
+-
+
+
+ setup(
+@@ -59,7 +35,7 @@ setup(
+ author='Aurélien Ginolhac, Mikkel Schubert, Hákon Jónsson',
+ author_email='MSchubert at snm.ku.dk, jonsson.hakon at gmail.com',
+ packages=['mapdamage'],
+- package_data={'mapdamage': ['Rscripts/*.R','Rscripts/stats/*.R','seqtk/seqtk']},
++ package_data={'mapdamage': ['Rscripts/*.R','Rscripts/stats/*.R']},
+ scripts=['bin/mapDamage'],
+ url='https://github.com/ginolhac/mapDamage',
+ license='LICENSE.txt',
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..441c30d
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,6 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+ dh $@ --with python2
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..404165a
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Hákon Jónsson and Aurélien Ginolhac and Mikkel Schubert and Philip Johnson and Ludovic Orlando
+ Title: "mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters"
+ Journal: Bioinformatics
+ Year: 2013
+ Volume: 29
+ Number: 13
+ Pages: 1682-4
+ DOI: 10.1093/bioinformatics/btt193
+ PMID: 23613487
+ URL: http://bioinformatics.oxfordjournals.org/content/early/2013/04/23/bioinformatics.btt193.abstract
+ eprint: http://bioinformatics.oxfordjournals.org/content/early/2013/04/23/bioinformatics.btt193.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..ba74445
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+ https://github.com/ginolhac/mapDamage/releases .*/archive/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
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