[med-svn] [mapping-pipeline] 02/10: Initual packaging

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository mapping-pipeline.

commit 3d0096613194ddda9c7479ad7a13ab217c7988d5
Author: Andreas Tille <tille at debian.org>
Date:   Mon Dec 12 13:23:20 2016 +0100

    Initual packaging
---
 debian/changelog             |  5 +++++
 debian/compat                |  1 +
 debian/control               | 30 ++++++++++++++++++++++++++++++
 debian/copyright             | 16 ++++++++++++++++
 debian/examples              |  1 +
 debian/install               |  4 ++++
 debian/links                 |  1 +
 debian/patches/python3.patch | 13 +++++++++++++
 debian/patches/series        |  1 +
 debian/rules                 |  7 +++++++
 debian/source/format         |  1 +
 debian/watch                 |  3 +++
 12 files changed, 83 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..76cf5a5
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+mapping-pipeline (1.2.0-1) UNRELEASED; urgency=medium
+
+  * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org>  Tue, 29 Nov 2016 16:34:36 +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..58921cd
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,30 @@
+Source: mapping-pipeline
+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),
+               dh-python,
+               python3-all
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/mapping-pipeline.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/mapping-pipeline.git
+Homepage: https://gitlab.com/RKIBioinformaticsPipelines/Mapping
+X-Python-Version: >= 3.4
+
+Package: mapping-pipeline
+Architecture: all
+Depends: ${python3:Depends},
+         ${misc:Depends},
+         bowtie2,
+         bwa,
+         samtools,
+         picard-tools,
+         python3-jinja2,
+         python3-matplotlib,
+         python3-scipy,
+         python3-pysam
+Description: Pipeline to map genomic reads
+ The mapping pipeline can be used together with either bowtie2 or bwa.
+ It is using either unpaired reads, first mate of paired read or a (set
+ of) project folder(s).
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..b56f909
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,16 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Mapping
+Upstream-Contact: Enrico Seiler <SeilerE at rki.de>
+Source: https://gitlab.com/RKIBioinformaticsPipelines/Mapping/tags
+
+Files: *
+Copyright: 2016 Enrico Seiler <SeilerE at rki.de>
+License: LGPL-3+
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <TilleA at rki.de>
+License: LGPL-3+
+
+License: LGPL-3+
+ On Debian Systems you can find a copy of the GNU Lesser General Public
+ License Version 3 at /usr/share/common-licenses/LGPL-3.
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..8010329
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1 @@
+example.*
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..772b183
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,4 @@
+*.py	usr/share/mapping-pipeline
+*.cwl	usr/share/mapping-pipeline
+*.tex	usr/share/mapping-pipeline
+
diff --git a/debian/links b/debian/links
new file mode 100644
index 0000000..7a7e48c
--- /dev/null
+++ b/debian/links
@@ -0,0 +1 @@
+usr/share/mapping-pipeline/mapping.py	usr/bin/mapping-pipeline
diff --git a/debian/patches/python3.patch b/debian/patches/python3.patch
new file mode 100644
index 0000000..a5ad17b
--- /dev/null
+++ b/debian/patches/python3.patch
@@ -0,0 +1,13 @@
+Author: Andreas Tille
+Last-Update: Mon, 12 Dec 2016 13:19:31 +0100
+Description: This script should not be called directly
+ (and if ever not with Python but rather Python3)
+
+--- a/metrics.py
++++ b/metrics.py
+@@ -1,5 +1,3 @@
+-#!/usr/bin/env python
+-
+ import custom_logger as log
+ import numpy as np
+ import matplotlib
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..a2fba86
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+python3.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..0ba4b3f
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,7 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+	dh $@ --with python3 # --buildsystem=pybuild
+
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/watch b/debian/watch
new file mode 100644
index 0000000..85d1a66
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=4
+opts="filenamemangle=s/.*\.tar\.gz\?ref=v?(\d\S*)/Mapping-$1\.tar\.gz/g,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+  https://gitlab.com/RKIBioinformaticsPipelines/Mapping/tags .*archive\.tar\.gz\?ref=v?(\d\S*)

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