[med-svn] [paleomix] 02/04: Initial packaging
Andreas Tille
tille at debian.org
Tue Feb 14 15:37:18 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository paleomix.
commit 63924eea9fe9939e33ad6ca8458b001f34a2e397
Author: Andreas Tille <tille at debian.org>
Date: Tue Feb 14 16:02:09 2017 +0100
Initial packaging
---
debian/changelog | 5 ++
debian/compat | 1 +
debian/control | 54 ++++++++++++++++++++++
debian/copyright | 39 ++++++++++++++++
.../patches/avoid_downloading_prerequisites.patch | 19 ++++++++
debian/patches/fix_makefile_test.patch | 32 +++++++++++++
debian/patches/series | 3 ++
debian/patches/work_around_os.getlogin.patch | 35 ++++++++++++++
debian/rules | 10 ++++
debian/source/format | 1 +
debian/upstream/metadata | 11 +++++
debian/watch | 3 ++
12 files changed, 213 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..98df5a2
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+paleomix (1.2.7-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Tue, 14 Feb 2017 12:04:19 +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..2d6e5fc
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,54 @@
+Source: paleomix
+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,
+ python,
+ python-setuptools,
+ python-coverage,
+ python-flexmock,
+ python-nose,
+ python-pysam,
+ python-setproctitle,
+ default-jre-headless,
+ bowtie2
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/paleomix.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/paleomix.git
+Homepage: http://geogenetics.ku.dk/publications/paleomix
+
+Package: paleomix
+Architecture: all
+Depends: ${misc:Depends},
+ ${python:Depends},
+ adapterremoval,
+ bedtools,
+ bowtie2,
+ bwa,
+ bcftools,
+ mafft,
+ mapdamage,
+ phylip,
+ picard-tools,
+ raxml,
+ samtools
+Suggests: examl
+Description: pipelines and tools for the processing of ancient and modern HTS data
+ The PALEOMIX pipelines are a set of pipelines and tools designed to aid
+ the rapid processing of High-Throughput Sequencing (HTS) data: The BAM
+ pipeline processes de-multiplexed reads from one or more samples,
+ through sequence processing and alignment, to generate BAM alignment
+ files useful in downstream analyses; the Phylogenetic pipeline carries
+ out genotyping and phylogenetic inference on BAM alignment files, either
+ produced using the BAM pipeline or generated elsewhere; and the Zonkey
+ pipeline carries out a suite of analyses on low coverage equine
+ alignments, in order to detect the presence of F1-hybrids in
+ archaeological assemblages. In addition, PALEOMIX aids in metagenomic
+ analysis of the extracts.
+ .
+ The pipelines have been designed with ancient DNA (aDNA) in mind, and
+ includes several features especially useful for the analyses of ancient
+ samples, but can all be for the processing of modern samples, in order
+ to ensure consistent data processing.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..4dbaa05
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,39 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: PALEOMIX
+Upstream-Contact: https://github.com/MikkelSchubert/paleomix/issues
+Source: https://github.com/MikkelSchubert/paleomix/releases
+
+Files: *
+Copyright: 2014-2017 Mikkel Schubert
+License: MIT
+
+Files: paleomix/yaml/*
+Copyright: 2006-2011 Kirill Simonov
+License: MIT
+Comment: This copy of yaml contains a few patches compared to the
+ Debian packaged version of yaml. Its not fully clear whether this is
+ really needed.
+ TODO: Ask upstream to forward the changes to pyyaml upstream
+
+Files: debian/*
+Copyright: 2017 Andreas Tille <tille at debian.org>
+License: MIT
+
+License: MIT
+ 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/avoid_downloading_prerequisites.patch b/debian/patches/avoid_downloading_prerequisites.patch
new file mode 100644
index 0000000..3b46861
--- /dev/null
+++ b/debian/patches/avoid_downloading_prerequisites.patch
@@ -0,0 +1,19 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 14 Feb 2017 12:04:19 +0100
+Description: Clean target tries to download python-coverage - just avoid this
+
+--- a/setup.py
++++ b/setup.py
+@@ -82,9 +82,9 @@ setup(
+ 'setproctitle>=1.1.0'],
+
+ # Dependencies set in setup_requires to allow use of 'setup.py nosetests'
+- setup_requires=['nose>=1.3.0',
+- 'flexmock>=0.9.7',
+- 'coverage>=4.0.0'],
++# setup_requires=['nose>=1.3.0',
++# 'flexmock>=0.9.7',
++# 'coverage>=4.0.0'],
+
+ test_suite='nose.collector',
+
diff --git a/debian/patches/fix_makefile_test.patch b/debian/patches/fix_makefile_test.patch
new file mode 100644
index 0000000..c2302b4
--- /dev/null
+++ b/debian/patches/fix_makefile_test.patch
@@ -0,0 +1,32 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 14 Feb 2017 12:04:19 +0100
+Description: Avoid test failure
+ ======================================================================
+ FAIL: common_tests.makefile_test.test_read_makefile__missing_simple_file
+ ----------------------------------------------------------------------
+ Traceback (most recent call last):
+ File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
+ self.test(*self.arg)
+ File "/build/paleomix-1.2.7/.pybuild/pythonX.Y_2.7/build/tests/common_tests/makefile_test.py", line 1650, in test_read_makefile__missing_simple_file
+ assert_equal(expected, result)
+ AssertionError: {'Statistics': {'MTime': '2005-07-07 08:50:00', 'Hash': '563a2052b67dcde9f193fbe [truncated]... != {'Statistics': {'MTime': '2005-07-07 06:50:00', 'Hash': '563a2052b67dcde9f193fbe [truncated]...
+ {'Makefile': {'Defaults': {'First': 0.0001, 'Second': 'a string'}},
+ 'Statistics': {'Filename': '/build/paleomix-1.2.7/.pybuild/pythonX.Y_2.7/build/tests/data/simple.yaml',
+ 'Hash': '563a2052b67dcde9f193fbe8d51fa2b6f0806505',
+ - 'MTime': '2005-07-07 08:50:00'}}
+ ? ^
+
+ + 'MTime': '2005-07-07 06:50:00'}}
+ ? ^
+
+--- a/tests/common_tests/makefile_test.py
++++ b/tests/common_tests/makefile_test.py
+@@ -1643,7 +1643,7 @@ def test_read_makefile__missing_simple_f
+ "Statistics": {
+ "Filename": test_file("simple.yaml"),
+ "Hash": "563a2052b67dcde9f193fbe8d51fa2b6f0806505",
+- "MTime": "2005-07-07 08:50:00",
++ "MTime": "2005-07-07 06:50:00",
+ }
+ }
+ result = read_makefile(test_file("simple.yaml"), specs)
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..c186495
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,3 @@
+avoid_downloading_prerequisites.patch
+fix_makefile_test.patch
+work_around_os.getlogin.patch
diff --git a/debian/patches/work_around_os.getlogin.patch b/debian/patches/work_around_os.getlogin.patch
new file mode 100644
index 0000000..34378b8
--- /dev/null
+++ b/debian/patches/work_around_os.getlogin.patch
@@ -0,0 +1,35 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 14 Feb 2017 12:04:19 +0100
+Description: Avoid test failures
+ ======================================================================
+ ERROR: Failure: OSError ([Errno 25] Inappropriate ioctl for device)
+ ----------------------------------------------------------------------
+ Traceback (most recent call last):
+ File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 418, in loadTestsFromName
+ addr.filename, addr.module)
+ File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
+ return self.importFromDir(dir_path, fqname)
+ File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
+ mod = load_module(part_fqname, fh, filename, desc)
+ File "/build/paleomix-1.2.7/.pybuild/pythonX.Y_2.7/build/tests/atomiccmd_test/command_test.py", line 164, in <module>
+ @with_temp_folder
+ File "paleomix/common/testing.py", line 49, in with_temp_folder
+ temp_root = os.path.join(tempfile.gettempdir(), os.getlogin())
+ OSError: [Errno 25] Inappropriate ioctl for device
+
+--- a/paleomix/common/testing.py
++++ b/paleomix/common/testing.py
+@@ -46,7 +46,12 @@ def with_temp_folder(func):
+ Creates a unique temporary folder before running 'func'. The
+ function is is assumed to take at least one parameter, the first
+ of which is assumed to represent the temporary folder."""
+- temp_root = os.path.join(tempfile.gettempdir(), os.getlogin())
++ try:
++ os_getlogin=os.getlogin()
++ except OSError: # see https://stackoverflow.com/questions/3100750/running-command-in-background
++ import pwd
++ os_getlogin=pwd.getpwuid(os.getuid()).pw_name
++ temp_root = os.path.join(tempfile.gettempdir(), os_getlogin)
+ make_dirs(temp_root) # Ensure that this subdirectory exists
+
+ @nose.tools.istest
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..101e20b
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,10 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+%:
+ dh $@ --with python2 --buildsystem=pybuild
+
+override_dh_auto_test:
+ PATH=$(CURDIR)/bin/:$(PATH) dh_auto_test
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..6e97877
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,11 @@
+Reference:
+ Author: Mikkel Schubert and Luca Ermini and Clio Der Sarkissian and Hákon Jónsson and Aurélien Ginolhac and Robert Schaefer and Michael D Martin and Ruth Fernández and Martin Kircher and Molly McCue and Eske Willerslev and Ludovic Orlando
+ Title: "Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX"
+ Journal: Nature Protocols
+ Year: 2014
+ Volume: 9
+ Number: 5
+ Pages: 1056-82
+ DOI: 10.1038/nprot.2014.063
+ PMID: 24722405
+ URL: http://www.nature.com/nprot/journal/v9/n5/full/nprot.2014.063.html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..5556144
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=4
+
+https://github.com/MikkelSchubert/paleomix/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
--
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