[med-svn] [macs2] 01/01: initial packaging

Michael Crusoe misterc-guest at moszumanska.debian.org
Sun Oct 4 06:15:30 UTC 2015


This is an automated email from the git hooks/post-receive script.

misterc-guest pushed a commit to branch master
in repository macs2.

commit 022b10112e8b64b562ae4337fe0a8744ce739eb1
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Sat Oct 3 10:41:47 2015 -0700

    initial packaging
---
 debian/changelog                |  5 +++
 debian/compat                   |  1 +
 debian/control                  | 32 +++++++++++++++++++
 debian/copyright                | 66 +++++++++++++++++++++++++++++++++++++++
 debian/lintian-overrides        |  1 +
 debian/manpages                 | 13 ++++++++
 debian/patches/series           |  1 +
 debian/patches/spelling         | 69 +++++++++++++++++++++++++++++++++++++++++
 debian/rules                    | 35 +++++++++++++++++++++
 debian/source/format            |  1 +
 debian/upstream/metadata        | 13 ++++++++
 debian/upstream/signing-key.asc | 50 +++++++++++++++++++++++++++++
 debian/watch                    |  3 ++
 13 files changed, 290 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..f3b0e5b
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+macs2 (2.1.0.20150731-1) UNRELEASED; urgency=low
+
+  * Initial release (Closes: #800828)
+
+ -- Michael R. Crusoe <crusoe at ucdavis.edu>  Sat, 03 Oct 2015 10:37:31 -0700
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..0288d19
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,32 @@
+Source: macs2
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Michael R. Crusoe <crusoe at ucdavis.edu>
+Build-Depends: debhelper (>= 9),
+               dh-python,
+               python-all-dev,
+               python-numpy,
+               python-setuptools,
+               help2man,
+               cython
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/macs2.git
+Vcs-Git: git://anonscm.debian.org/debian-med/macs2.git
+Homepage: http://github.com/taoliu/MACS/
+
+Package: macs2
+Architecture: any
+Depends: ${python:Depends}, ${shlibs:Depends}, ${misc:Depends}
+Description: Model Based Analysis for ChIP-Seq data
+ With the improvement of sequencing techniques, chromatin
+ immunoprecipitation followed by high throughput sequencing (ChIP-Seq)
+ is getting popular to study genome-wide protein-DNA interactions. To
+ address the lack of powerful ChIP-Seq analysis method, here is a
+ novel algorithm, named Model-based Analysis of ChIP-Seq (MACS), for
+ identifying transcript factor binding sites. MACS captures the
+ influence of genome complexity to evaluate the significance of
+ enriched ChIP regions, and MACS improves the spatial resolution of
+ binding sites through combining the information of both sequencing tag
+ position and orientation. MACS can be easily used for ChIP-Seq data
+ alone, or with control sample with the increase of specificity.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..53d365c
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,66 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: MACS2
+Source: https://github.com/taoliu/MACS
+
+Files: *
+Copyright: © 2008-2013 Tao Liu lab at UB and Xiaole Shirley Liu lab at DFCI
+           2008-2009 Yong Zhang, Tao Liu <taoliu at jimmy.harvard.edu>
+           2010-2011 Tao Liu <taoliu at jimmy.harvard.edu>
+           2014, Tao Liu <tliu4 at buffalo.edu>
+           2010-2013, Tao Liu <vladimir.liu at gmail.com>
+           2008-2011, Hyunjin Shin, Tao Liu <taoliu at jimmy.harvard.edu>
+License: BSD-3-clause
+
+Files: debian/*
+Copyright: © 2015 Michael R. Crusoe <crusoe at ucdavis.edu>
+License: BSD-3-clause
+
+Files: MACS2/khash.h
+Copyright: 2008, 2009, 2011 Attractive Chaos <attractor at live.co.uk>
+License: Expat
+
+License: BSD-3-clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+     * Redistributions of source code must retain the above copyright
+       notice, this list of conditions and the following disclaimer.
+     * Redistributions in binary form must reproduce the above copyright
+       notice, this list of conditions and the following disclaimer in the
+       documentation and/or other materials provided with the distribution.
+     * Neither the name of Tao Liu lab or Xiaole Shirley Liu lab nor the
+       names of its contributors may be used to endorse or promote products
+       derived from this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL COPYRIGHT
+ HOLDERs AND CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+ INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+ BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
+ OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
+ TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
+ USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+ DAMAGE.
+
+License: Expat
+   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/lintian-overrides b/debian/lintian-overrides
new file mode 100644
index 0000000..019e589
--- /dev/null
+++ b/debian/lintian-overrides
@@ -0,0 +1 @@
+macs2: manpage-has-errors-from-man usr/share/man/man1/macs2.1.gz 8: warning [p 1, 1.7i]: cannot adjust line
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..289107d
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1,13 @@
+debian/macs2.1
+debian/macs2_bdgbroadcall.1
+debian/macs2_bdgcmp.1
+debian/macs2_bdgdiff.1
+debian/macs2_bdgopt.1
+debian/macs2_bdgpeakcall.1
+debian/macs2_callpeak.1
+debian/macs2_cmbreps.1
+debian/macs2_filterdup.1
+debian/macs2_pileup.1
+debian/macs2_predictd.1
+debian/macs2_randsample.1
+debian/macs2_refinepeak.1
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..e057d52
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+spelling
diff --git a/debian/patches/spelling b/debian/patches/spelling
new file mode 100644
index 0000000..fa5699f
--- /dev/null
+++ b/debian/patches/spelling
@@ -0,0 +1,69 @@
+Author: Michael R. Crusoe <crusoe at ucdavis.edu>
+Description: Fix spelling erorr
+--- macs2.orig/MACS2/PeakModel.pyx
++++ macs2/MACS2/PeakModel.pyx
+@@ -559,7 +559,7 @@
+     This method is based on the convolution of a scaled window with the signal.
+     The signal is prepared by introducing reflected copies of the signal 
+     (with the window size) in both ends so that transient parts are minimized
+-    in the begining and end part of the output signal.
++    in the beginning and end part of the output signal.
+     
+     input:
+         x: the input signal 
+--- macs2.orig/bin/macs2
++++ macs2/bin/macs2
+@@ -370,7 +370,7 @@
+     """Add function 'peak calling on bedGraph' argument parsers.
+     """    
+     argparser_bdgpeakcall = subparsers.add_parser( "bdgpeakcall",
+-                                                   help = "Call peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
++                                                   help = "Call peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
+     argparser_bdgpeakcall.add_argument( "-i", "--ifile", dest = "ifile", type = str, required = True,
+                                         help = "MACS score in bedGraph. REQUIRED" )
+     argparser_bdgpeakcall.add_argument( "-c", "--cutoff" , dest = "cutoff", type = float,
+@@ -395,7 +395,7 @@
+     """Add function 'broad peak calling on bedGraph' argument parsers.
+     """
+     argparser_bdgbroadcall = subparsers.add_parser( "bdgbroadcall",
+-                                                    help = "Call broad peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
++                                                    help = "Call broad peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
+     argparser_bdgbroadcall.add_argument( "-i", "--ifile", dest = "ifile" , type = str, required = True,
+                                          help = "MACS score in bedGraph. REQUIRED" )
+     argparser_bdgbroadcall.add_argument( "-c", "--cutoff-peak", dest = "cutoffpeak", type = float,
+@@ -418,7 +418,7 @@
+     """Add function 'peak calling on bedGraph' argument parsers.
+     """
+     argparser_bdgcmp = subparsers.add_parser( "bdgcmp",
+-                                              help = "Deduct noise by comparing two signal tracks in bedGraph. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
++                                              help = "Deduct noise by comparing two signal tracks in bedGraph. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
+     argparser_bdgcmp.add_argument( "-t", "--tfile", dest = "tfile", type = str, required = True,
+                                    help = "Treatment bedGraph file, e.g. *_treat_pileup.bdg from MACSv2. REQUIRED")
+     argparser_bdgcmp.add_argument( "-c", "--cfile", dest = "cfile", type = str, required = True,
+@@ -444,7 +444,7 @@
+     """Add function 'operations on score column of bedGraph' argument parsers.
+     """    
+     argparser_bdgopt = subparsers.add_parser( "bdgopt",
+-                                              help = "Operations on score column of bedGraph file. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
++                                              help = "Operations on score column of bedGraph file. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
+     argparser_bdgopt.add_argument( "-i", "--ifile", dest = "ifile", type = str, required = True,
+                                    help = "MACS score in bedGraph. Note: this must be a bedGraph file covering the ENTIRE genome. REQUIRED" )
+     argparser_bdgopt.add_argument( "-m", "--method", dest = "method", type = str,
+@@ -461,7 +461,7 @@
+     """Add function 'combine replicates' argument parsers.
+     """
+     argparser_cmbreps = subparsers.add_parser( "cmbreps",
+-                                               help = "Combine BEDGraphs of scores from replicates. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
++                                               help = "Combine BEDGraphs of scores from replicates. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
+     argparser_cmbreps.add_argument( "-i", dest = "ifile", type = str, required = True, nargs = "+",
+                                     help = "MACS score in bedGraph for each replicate. Require exactly two files such as '-i A B'. REQUIRED" )
+     # argparser_cmbreps.add_argument( "-w", dest = "weights", type = float, nargs = "*",
+@@ -503,7 +503,7 @@
+     
+ def add_bdgdiff_parser( subparsers ):
+     argparser_bdgdiff = subparsers.add_parser( "bdgdiff",
+-                                               help = "Differential peak detection based on paired four bedgraph files. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
++                                               help = "Differential peak detection based on paired four bedgraph files. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
+     argparser_bdgdiff.add_argument( "--t1", dest = "t1bdg", type = str, required = True,
+                                     help = "MACS pileup bedGraph for condition 1. Incompatible with callpeak --SPMR output. REQUIRED" )
+     argparser_bdgdiff.add_argument( "--t2", dest="t2bdg", type = str, required = True,
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..9076306
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,35 @@
+#!/usr/bin/make -f
+
+export PYBUILD_NAME=MACS2
+DEBVERS        := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+VERSION        := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+subcommands=callpeak bdgpeakcall bdgbroadcall bdgcmp bdgopt cmbreps bdgdiff \
+	      filterdup predictd pileup randsample refinepeak
+tagline=\- Model\-based Analysis for ChIP\-Sequencing
+# DH_VERBOSE := 1
+
+%:
+	dh $@ --with python2 --buildsystem=pybuild
+
+override_dh_auto_build:
+	for pyx in `find MACS2/ -name "*.pyx" | grep -v khash`; do \
+		rm -f $${pyx%%.pyx}.{h,c}; touch $${pyx}; done
+	cp setup.py setup.py.orig
+	cp setup_w_cython.py setup.py
+	dh_auto_build
+	PYTHONPATH=./.pybuild/pythonX.Y_2.7/build/ help2man \
+		--no-discard-stderr --no-info \
+		--name "macs2 ${tagline}" "python bin/macs2" > debian/macs2.1
+	for subcommand in ${subcommands}; do printf \
+		"[NAME]\nmacs2_$${subcommand} ${tagline}\n" \
+		> debian/macs2_$${subcommand}-man-include; done
+	for subcommand in ${subcommands}; do \
+		PYTHONPATH=./.pybuild/pythonX.Y_2.7/build/ help2man \
+		--no-discard-stderr --no-info --version-string="$(VERSION)" \
+		--include debian/macs2_$${subcommand}-man-include \
+		"python bin/macs2 $${subcommand}" > \
+		debian/macs2_$${subcommand}.1; done
+
+override_dh_auto_clean:
+	dh_auto_clean
+	rm -f debian/*.1 debian/*-man-include
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..f0f7968
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,13 @@
+Reference:
+  Author: Yong Zhang and Tao Liu and Clifford A Meyer and J{\'{e}}r{\^{o}}me
+Eeckhoute and David S Johnson and Bradley E Bernstein and Chad Nussbaum and
+Richard M Myers and Myles Brown and Wei Li and X Shirley Liu
+  Title: Model-based Analysis of {ChIP}-Seq ({MACS})
+  Journal: Genome Biol
+  Year: 2008
+  Volume: 9
+  Number: 9
+  Pages: R137
+  DOI: 10.1186/gb-2008-9-9-r137
+  PMID: 18798982
+  URL: http://dx.doi.org/10.1186/gb-2008-9-9-r137
diff --git a/debian/upstream/signing-key.asc b/debian/upstream/signing-key.asc
new file mode 100644
index 0000000..09bf30f
--- /dev/null
+++ b/debian/upstream/signing-key.asc
@@ -0,0 +1,50 @@
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diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..b25ab49
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+opts=uversionmangle=s/(rc|a|b|c)/~$1/,pgpsigurlmangle=s/$/.asc/ \
+https://pypi.debian.net/MACS2/MACS2-(.+)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))

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