[med-svn] [cnvkit] 02/02: initial Debianization
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sun Jun 26 01:50:03 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository cnvkit.
commit 0242aada7f5e915c718f727286ed660eb76370d7
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Sat Jun 25 11:02:04 2016 -0700
initial Debianization
---
debian/changelog | 5 ++++
debian/clean | 2 ++
debian/compat | 1 +
debian/control | 34 ++++++++++++++++++++++++++++
debian/copyright | 27 ++++++++++++++++++++++
debian/genmanpages.py | 21 +++++++++++++++++
debian/manpages | 1 +
debian/patches/no-py-ext | 13 +++++++++++
debian/patches/series | 1 +
debian/rules | 59 ++++++++++++++++++++++++++++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++++++++
debian/watch | 7 ++++++
13 files changed, 184 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..6e13a11
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+cnvkit (0.7.11-1) UNRELEASED; urgency=medium
+
+ * Initial release. (Closes: #828176)
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Sat, 25 Jun 2016 10:57:17 -0700
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..991ead8
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1,2 @@
+debian/*.1
+debian/*.include
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..e9a3996
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,34 @@
+Source: cnvkit
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Michael R. Crusoe <michael.crusoe at gmail.com>
+Build-Depends: debhelper (>= 9),
+ dh-python,
+ python-all,
+ python-setuptools,
+ python-pyfaidx,
+ help2man,
+ python-biopython,
+ python-pandas,
+ python-numpy,
+ python-pysam,
+ python-scipy,
+ python-matplotlib,
+ python-pyvcf,
+ r-cran-pscbs,
+ python-subprocess32
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/cnvkit.git
+Vcs-Git: https://anonscm.debian.org/debian-med/cnvkit.git
+Homepage: http://cnvkit.readthedocs.org
+X-Python-Version: >= 2.7
+
+Package: cnvkit
+Architecture: all
+Depends: ${python:Depends}, ${misc:Depends}
+Description: Copy number variant detection from targeted DNA sequencing
+ A command-line toolkit and Python library for detecting copy number variants
+ and alterations genome-wide from targeted DNA sequencing. It is designed for
+ use with hybrid capture, including both whole-exome and custom target panels,
+ and short-read sequencing platforms such as Illumina and Ion Torrent.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..919a84b
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,27 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: cnvkit
+Source: https://github.com/etal/cnvkit
+
+Files: *
+Copyright: © 2013-2017 Eric Talevich
+License: Apache-2.0
+
+Files: debian/*
+Copyright: © 2016 Michael R. Crusoe <michael.crusoe at gmail.com>
+License: Apache-2.0
+
+License: Apache-2.0
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+ .
+ http://www.apache.org/licenses/LICENSE-2.0
+ .
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+ .
+ On Debian systems, the full text of the Apache License, Version 2.0 can be
+ found in the file `/usr/share/common-licenses/Apache-2.0'
diff --git a/debian/genmanpages.py b/debian/genmanpages.py
new file mode 100755
index 0000000..9745403
--- /dev/null
+++ b/debian/genmanpages.py
@@ -0,0 +1,21 @@
+#!/usr/bin/python
+from __future__ import print_function
+from cnvlib import commands
+import os
+import sys
+if os.name == 'posix' and sys.version_info[0] < 3:
+ import subprocess32 as subprocess
+else:
+ import subprocess
+
+for subcommand in commands.AP_subparsers._get_subactions():
+ name = subcommand.dest
+ description = subcommand.help
+ if name == 'version':
+ break
+ with open("debian/cnvkit-%s.man.include" % name, "w") as f:
+ print("[NAME]", file=f)
+ print("cnvkit_%s \- %s" % (name, description), file=f)
+ subprocess.check_call(['help2man', '--no-info', '--version-string=%s'
+ % sys.argv[1], '--include=debian/cnvkit-%s.man.include' % name,
+ '--output=debian/cnvkit-%s.1' % name, './cnvkit %s' % name])
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1
diff --git a/debian/patches/no-py-ext b/debian/patches/no-py-ext
new file mode 100644
index 0000000..4d1f624
--- /dev/null
+++ b/debian/patches/no-py-ext
@@ -0,0 +1,13 @@
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Description: Remove .py extensions as per Debian policy
+--- cnvkit.orig/setup.py
++++ cnvkit/setup.py
+@@ -41,7 +41,7 @@
+ 'cnvlib.ngfrills',
+ 'cnvlib.segmentation',
+ ],
+- scripts=[join(DIR, 'cnvkit.py')] + glob(join(DIR, 'scripts/*.py')),
++ scripts=[join(DIR, 'cnvkit')] + glob(join(DIR, 'scripts/*')),
+ classifiers=[
+ "Development Status :: 4 - Beta",
+ "Environment :: Console",
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..263d233
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+no-py-ext
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..c5d8ae2
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,59 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+export PYBUILD_NAME=cnvkit
+# some helpful variables - uncomment them if needed
+# shamelessly stolen from http://jmtd.net/log/awk/
+DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
+#GIT_TAG := $(subst ~,_,$(VERSION))
+
+# alternatively to manually set those variables, you can
+# include /usr/share/dpkg/default.mk
+# and use what is set there.
+
+# for hardening you might like to uncomment this:
+# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+%:
+ dh $@ --with python2 --buildsystem=pybuild
+
+override_dh_auto_build:
+ mv cnvkit.py cnvkit
+ mv scripts/genome2access.py ./
+ cd scripts; for script in *.py; do mv $${script} \
+ cnvkit-$${script%%.py}; done
+ dh_auto_build
+ cd scripts; for script in *; do mv $${script} $${script##cnvkit-}.py; \
+ done
+ mv cnvkit cnvkit.py
+ mv genome2access.py scripts/
+
+override_dh_auto_install:
+ mv cnvkit.py cnvkit
+ mv scripts/genome2access.py ./
+ cd scripts; for script in *.py; do mv $${script} \
+ cnvkit-$${script%%.py}; done
+ dh_auto_install
+ help2man --no-info --version-option=version \
+ --name="a command-line toolkit for copy number analysis." \
+ ./cnvkit > debian/cnvkit.1
+ debian/genmanpages.py ${VERSION}
+ cd scripts; for script in *; do PYTHONPATH=../ help2man --no-info \
+ --version-string=${VERSION} --help-option='-h' ./$${script} > \
+ ../debian/$${script}.1; done
+ cd scripts; for script in *; do mv $${script} $${script##cnvkit-}.py; \
+ done
+ mv cnvkit cnvkit.py
+ mv genome2access.py scripts/
+
+override_dh_auto_test:
+ cd test; ${MAKE}
+
+override_dh_auto_clean:
+ cd test && ${MAKE} clean || /bin/true
+ dh_auto_clean
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..d8b5812
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author:
+ Title:
+ Journal:
+ Year:
+ Volume:
+ Number:
+ Pages:
+ DOI:
+ PMID:
+ URL:
+ eprint:
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..d14114e
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,7 @@
+version=3
+
+# Uncomment to find new files on Github
+# - when using releases:
+https://github.com/etal/cnvkit/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+# if you need to repack and choose +dfsg prefix
+# opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,compress=xz" \
--
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