[med-svn] [toil] 02/02: Initial release.
Steffen Möller
moeller at moszumanska.debian.org
Sun Jan 15 08:04:16 UTC 2017
This is an automated email from the git hooks/post-receive script.
moeller pushed a commit to branch master
in repository toil.
commit 9f00fae0b31231119692bf01ae760c663cfc66ed
Author: Steffen Moeller <moeller at debian.org>
Date: Sun Jan 15 08:41:40 2017 +0100
Initial release.
---
debian/README.Debian | 11 ++++++++
debian/README.source | 10 +++++++
debian/changelog | 5 ++++
debian/compat | 1 +
debian/control | 48 +++++++++++++++++++++++++++++++++
debian/copyright | 30 +++++++++++++++++++++
debian/patches/bd2k_as_short_name.patch | 13 +++++++++
debian/patches/series | 1 +
debian/python-toil.postinst | 7 +++++
debian/python-toil.prerm | 15 +++++++++++
debian/rules | 32 ++++++++++++++++++++++
debian/source/format | 1 +
debian/source/options | 1 +
debian/toil-docs.docs | 2 ++
debian/watch | 15 +++++++++++
15 files changed, 192 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..56fb748
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,11 @@
+toil for Debian
+---------------
+
+This package is still preliminary since
+ * testing is not activated
+ * it is awkward to have both python2 and python3 supported, left it with python2
+ * manpages are missing
+ * dependency on cgcloud https://github.com/BD2KGenomics/cgcloud not followed which ruins tests
+
+--
+ Steffen Moeller <moeller at debian.org> Sat, 14 Jan 2017 13:43:23 +0100
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..60d2966
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,10 @@
+toil for Debian
+---------------
+
+The current version the package was derived from what was uploaded to the
+pypi repository. This should be changed towards the gihub repository,
+except for a lack of tags that are not set for the latest versions
+available on Pypi.
+
+ -- Steffen Moeller <moeller at debian.org> Fri, 13 Jan 2017 15:58:18 +0100
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..54e1f97
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+toil (3.5.0~alpha1.321-1) unstable; urgency=medium
+
+ * Initial release (Closes: #851365)
+
+ -- Steffen Moeller <moeller at debian.org> Fri, 13 Jan 2017 15:58:18 +0100
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..8dba0aa
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,48 @@
+Source: toil
+Section: net
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 9), dh-python, python-all, python-setuptools, python3-all, python3-setuptools
+Standards-Version: 3.9.8
+Homepage: https://github.com/BD2KGenomics/toil
+X-Python-Version: >= 2.6
+#X-Python3-Version: >= 3.2
+Vcs-Git: https://anonscm.debian.org/git/debian-med/toil.git
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/toil.git
+#Testsuite: autopkgtest-pkg-python
+
+Package: python-toil
+Architecture: all
+Depends: ${python:Depends}, ${misc:Depends}, python-cgcloud-lib
+#Suggests: python-toil-doc
+Conflicts: python3-toil
+Description: cross-platform workflow engine (Python 2)
+ Toil is a scalable, efficient, cross-platform and easy-to-use workflow
+ engine in pure Python. It works with several well established load
+ balancers like Slurm or the Sun Grid Engine. Toil is compatible with
+ the Common Workflow Language (CWL).
+ .
+ This package installs the library for Python 2.
+
+#Package: python3-toil
+#Architecture: all
+#Depends: ${python3:Depends}, ${misc:Depends}
+#Suggests: python-toil-doc
+#Conflicts: python-toil
+#Description: cross-platform workflow engine (Python 3)
+# Toil is a scalable, efficient, cross-platform and easy-to-use workflow
+# engine in pure Python. It works with several well established load
+# balancers like Slurm or the Sun Grid Engine. Toil is compatible with
+# the Common Workflow Language (CWL).
+# .
+# This package installs the library for Python 3.
+
+#Package: python-toil-doc
+#Architecture: all
+#Section: doc
+#Depends: ${sphinxdoc:Depends}, ${misc:Depends}
+#Description: cross-platform workflow engine (common documentation)
+# The documentation of Toil shall go here at some point.
+# .
+# This is the common documentation package.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..dff32ca
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,30 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: toil
+Source: https://github.com/BD2KGenomics/toil
+Files-Excluded: src/toil.egg-info/*
+
+Files: *
+Copyright: Benedict Paten <benedict at soe.usc.edu>
+ 2015-2016 Regents of the University of California
+ 2015 UCSC Computational Genomics Lab
+License: Apache-2.0
+
+Files: debian/*
+Copyright: 2017 Steffen Moeller <moeller at debian.org>
+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
+ .
+ https://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 complete text of the Apache version 2.0 license
+ can be found in "/usr/share/common-licenses/Apache-2.0".
diff --git a/debian/patches/bd2k_as_short_name.patch b/debian/patches/bd2k_as_short_name.patch
new file mode 100644
index 0000000..e9caf35
--- /dev/null
+++ b/debian/patches/bd2k_as_short_name.patch
@@ -0,0 +1,13 @@
+Index: toil/setup.py
+===================================================================
+--- toil.orig/setup.py
++++ toil/setup.py
+@@ -30,7 +30,7 @@ def runSetup():
+ author_email='benedict at soe.usc.edu',
+ url="https://github.com/BD2KGenomics/toil",
+ install_requires=[
+- 'bd2k-python-lib>=1.14a1.dev35',
++ 'bd2k>=1.14a1.dev35',
+ 'dill==0.2.5',
+ 'six>=1.10.0'],
+ extras_require={
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..7aaeaf9
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+bd2k_as_short_name.patch
diff --git a/debian/python-toil.postinst b/debian/python-toil.postinst
new file mode 100644
index 0000000..7b28cd4
--- /dev/null
+++ b/debian/python-toil.postinst
@@ -0,0 +1,7 @@
+#!/bin/sh
+set -e
+
+update-alternatives --quiet --install /usr/bin/cwl-runner cwl-runner \
+ /usr/bin/cwl-runner-toil 1
+
+#DEBHELPER#
diff --git a/debian/python-toil.prerm b/debian/python-toil.prerm
new file mode 100644
index 0000000..d6c3c3c
--- /dev/null
+++ b/debian/python-toil.prerm
@@ -0,0 +1,15 @@
+#!/bin/sh
+set -e
+
+case "$1" in
+ remove)
+ update-alternatives --remove cwl-runner /usr/bin/cwl-runner-toil
+ ;;
+
+ upgrade|failed-upgrade|deconfigure)
+ ;;
+
+esac
+
+#DEBHELPER#
+
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..b3c7340
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,32 @@
+#!/usr/bin/make -f
+# See debhelper(7) (uncomment to enable)
+# output every command that modifies files on the build system.
+#export DH_VERBOSE = 1
+
+export PYBUILD_NAME=toil
+
+export PYBUILD_DESTDIR_python2=debian/python-toil/
+export PYBUILD_DESTDIR_python3=debian/python3-toil/
+
+export PYBUILD_DISABLE=test
+export PYBUILD_DISABLE_python3=1
+
+%:
+ dh $@ --with python2 --buildsystem=pybuild
+
+
+# If you need to rebuild the Sphinx documentation
+# Add spinxdoc to the dh --with line
+#override_dh_auto_build:
+# dh_auto_build
+# PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bhtml docs/ build/html # HTML generator
+# PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bman docs/ build/man # Manpage generator
+
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -rf src/toil.egg-info
+
+override_dh_install:
+ dh_install
+ mv $(CURDIR)/debian/python-toil/usr/bin/cwl-runner $(CURDIR)/debian/python-toil/usr/bin/cwl-runner-toil
+ #mv $(CURDIR)/debian/python3-toil/usr/bin/cwl-runner $(CURDIR)/debian/python3-toil/usr/bin/cwl-runner-toil
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/source/options b/debian/source/options
new file mode 100644
index 0000000..cb61fa5
--- /dev/null
+++ b/debian/source/options
@@ -0,0 +1 @@
+extend-diff-ignore = "^[^/]*[.]egg-info/"
diff --git a/debian/toil-docs.docs b/debian/toil-docs.docs
new file mode 100644
index 0000000..efea0a6
--- /dev/null
+++ b/debian/toil-docs.docs
@@ -0,0 +1,2 @@
+README.Debian
+README.source
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..cf104b1
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,15 @@
+# Compulsory line, this is a version 4 file
+version=4
+
+# HTTP site (basic)
+#http://example.com/downloads.html \
+# files/toil-([\d\.]+)\.tar\.gz debian uupdate
+
+# GitHub hosted projects
+#opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%<project>-$1.tar.gz%" \
+# https://github.com/iBD2KGenomics/toil/tags \
+# (?:.*?/)?v?(\d[\d.]*)\.tar\.gz debian uupdate
+
+# PyPI
+opts="uversionmangle=s%a(\d).dev(?)%~alpha$1.$2%" \
+ https://pypi.debian.net/toil/toil-(.+)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
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