[med-svn] r18752 - in trunk/packages: . miso miso/trunk miso/trunk/debian miso/trunk/debian/source
Steffen Möller
moeller at moszumanska.debian.org
Wed Feb 11 09:43:52 UTC 2015
Author: moeller
Date: 2015-02-11 09:41:00 +0000 (Wed, 11 Feb 2015)
New Revision: 18752
Added:
trunk/packages/miso/
trunk/packages/miso/trunk/
trunk/packages/miso/trunk/debian/
trunk/packages/miso/trunk/debian/README.Debian
trunk/packages/miso/trunk/debian/changelog
trunk/packages/miso/trunk/debian/compat
trunk/packages/miso/trunk/debian/control
trunk/packages/miso/trunk/debian/copyright
trunk/packages/miso/trunk/debian/miso.doc-base.EX
trunk/packages/miso/trunk/debian/rules
trunk/packages/miso/trunk/debian/source/
trunk/packages/miso/trunk/debian/source/format
trunk/packages/miso/trunk/debian/watch.ex
Log:
Functional package for miso
Well, there is some work left to do, I would not
mind the package to be adopted by some good soul.
Issues:
* the binary package name should be python-misopy,
not python-miso
* debian/watch
* not lintian-clean
Cheers,
Steffen
Property changes on: trunk/packages/miso/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/miso/trunk/debian/README.Debian
===================================================================
--- trunk/packages/miso/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/miso/trunk/debian/README.Debian 2015-02-11 09:41:00 UTC (rev 18752)
@@ -0,0 +1,6 @@
+miso for Debian
+---------------
+
+Please consider adopting this package.
+
+ -- Steffen Moeller <moeller at debian.org> Tue, 10 Feb 2015 17:55:01 +0100
Added: trunk/packages/miso/trunk/debian/changelog
===================================================================
--- trunk/packages/miso/trunk/debian/changelog (rev 0)
+++ trunk/packages/miso/trunk/debian/changelog 2015-02-11 09:41:00 UTC (rev 18752)
@@ -0,0 +1,5 @@
+miso (0.5.2-1) unstable; urgency=low
+
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+
+ -- Steffen Moeller <moeller at debian.org> Tue, 10 Feb 2015 17:55:01 +0100
Added: trunk/packages/miso/trunk/debian/compat
===================================================================
--- trunk/packages/miso/trunk/debian/compat (rev 0)
+++ trunk/packages/miso/trunk/debian/compat 2015-02-11 09:41:00 UTC (rev 18752)
@@ -0,0 +1 @@
+9
Added: trunk/packages/miso/trunk/debian/control
===================================================================
--- trunk/packages/miso/trunk/debian/control (rev 0)
+++ trunk/packages/miso/trunk/debian/control 2015-02-11 09:41:00 UTC (rev 18752)
@@ -0,0 +1,45 @@
+Source: miso
+Section: science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 9~), dh-python, python-all (>= 2.6.6-3~), python-setuptools,
+ dpkg-dev (>= 1.16.1~)
+#, python3-all, python3-setuptools
+Standards-Version: 3.9.6
+Homepage: http://genes.mit.edu/burgelab/miso/
+X-Python-Version: >= 2.6
+#X-Python3-Version: >= 3.2
+#Vcs-Git: git://anonscm.debian.org/collab-maint/miso.git
+#Vcs-Browser: http://anonscm.debian.org/?p=collab-maint/miso.git;a=summary
+
+Package: python-miso
+Architecture: any
+Depends: ${shlibs:Depends}, ${python:Depends}, ${misc:Depends}
+Description: Mixture of Isoforms model for RNA-Seq isoform quantitation
+ MISO (Mixture of Isoforms) is a probabilistic framework that quantitates
+ the expression level of alternatively spliced genes from RNA-Seq
+ data, and identifies differentially regulated isoforms or exons across
+ samples. By modeling the generative process by which reads are produced
+ from isoforms in RNA-Seq, the MISO model uses Bayesian inference to
+ compute the probability that a read originated from a particular isoform.
+ .
+ MISO uses the inferred assignment of reads to isoforms to quantitate the
+ abundances of the underlying set of alternative mRNA isoforms. Confidence
+ intervals over estimates can be obtained, which quantify the reliability
+ of the estimates.
+
+#Package: python3-miso
+#Architecture: any
+#Depends: ${shlibs:Depends}, ${python3:Depends}, ${misc:Depends}
+#Description: Mixture of Isoforms model for RNA-Seq isoform quantitation
+# MISO (Mixture of Isoforms) is a probabilistic framework that quantitates
+# the expression level of alternatively spliced genes from RNA-Seq
+# data, and identifies differentially regulated isoforms or exons across
+# samples. By modeling the generative process by which reads are produced
+# from isoforms in RNA-Seq, the MISO model uses Bayesian inference to
+# compute the probability that a read originated from a particular isoform.
+# .
+# MISO uses the inferred assignment of reads to isoforms to quantitate the
+# abundances of the underlying set of alternative mRNA isoforms. Confidence
+# intervals over estimates can be obtained, which quantify the reliability
+# of the estimates.
Added: trunk/packages/miso/trunk/debian/copyright
===================================================================
--- trunk/packages/miso/trunk/debian/copyright (rev 0)
+++ trunk/packages/miso/trunk/debian/copyright 2015-02-11 09:41:00 UTC (rev 18752)
@@ -0,0 +1,28 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: miso
+Source: https://pypi.python.org/pypi/misopy
+
+Files: *
+Copyright: Yarden Katz <yarden at mit.edu>
+License: GPL-2.0+
+
+Files: debian/*
+Copyright: 2015 Steffen Moeller <moeller at debian.org>
+License: GPL-2.0+
+
+License: GPL-2.0+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
Added: trunk/packages/miso/trunk/debian/miso.doc-base.EX
===================================================================
--- trunk/packages/miso/trunk/debian/miso.doc-base.EX (rev 0)
+++ trunk/packages/miso/trunk/debian/miso.doc-base.EX 2015-02-11 09:41:00 UTC (rev 18752)
@@ -0,0 +1,20 @@
+Document: miso
+Title: Debian miso Manual
+Author: <insert document author here>
+Abstract: This manual describes what miso is
+ and how it can be used to
+ manage online manuals on Debian systems.
+Section: unknown
+
+Format: debiandoc-sgml
+Files: /usr/share/doc/miso/miso.sgml.gz
+
+Format: postscript
+Files: /usr/share/doc/miso/miso.ps.gz
+
+Format: text
+Files: /usr/share/doc/miso/miso.text.gz
+
+Format: HTML
+Index: /usr/share/doc/miso/html/index.html
+Files: /usr/share/doc/miso/html/*.html
Added: trunk/packages/miso/trunk/debian/rules
===================================================================
--- trunk/packages/miso/trunk/debian/rules (rev 0)
+++ trunk/packages/miso/trunk/debian/rules 2015-02-11 09:41:00 UTC (rev 18752)
@@ -0,0 +1,24 @@
+#!/usr/bin/make -f
+#DH_VERBOSE = 1
+
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/default.mk
+
+# see FEATURE AREAS in dpkg-buildflags(1)
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+# see ENVIRONMENT in dpkg-buildflags(1)
+# package maintainers to append CFLAGS
+#export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic
+# package maintainers to append LDFLAGS
+#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+
+#export PYBUILD_NAME=misopy
+
+%:
+ dh $@
+ #dh $@ --with python2,python3
+
+override_dh_clean:
+ rm -rf tmp a.out
+ dh_clean
Property changes on: trunk/packages/miso/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/miso/trunk/debian/source/format
===================================================================
--- trunk/packages/miso/trunk/debian/source/format (rev 0)
+++ trunk/packages/miso/trunk/debian/source/format 2015-02-11 09:41:00 UTC (rev 18752)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/miso/trunk/debian/watch.ex
===================================================================
--- trunk/packages/miso/trunk/debian/watch.ex (rev 0)
+++ trunk/packages/miso/trunk/debian/watch.ex 2015-02-11 09:41:00 UTC (rev 18752)
@@ -0,0 +1,4 @@
+version=3
+https://pypi.python.org/pypi/misopy misopy.nbsp.([0-9.]*)
+#http://www.example.com/downloads.php miso-(.*)\.tar\.gz
+#https://pypi.python.org/packages/source/m/misopy/misopy-(.*)\.tar\.gz
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