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commit 63924eea9fe9939e33ad6ca8458b001f34a2e397 Author: Andreas Tille <[email protected]> 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 <[email protected]> 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 <[email protected]> +Uploaders: Andreas Tille <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 <[email protected]> +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) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/paleomix.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
