[med-svn] [inspect] 02/02: Add initial packaging
Andreas Tille
tille at debian.org
Wed Sep 30 15:18:22 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository inspect.
commit ccb403a2ee0ba9d3ab8d1fd541d1d27e37c48d10
Author: Andreas Tille <tille at debian.org>
Date: Wed Sep 30 17:12:48 2015 +0200
Add initial packaging
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 55 ++++++++++++++++++++++++++++++++++++++++++++++++
debian/copyright | 41 ++++++++++++++++++++++++++++++++++++
debian/get-orig-source | 32 ++++++++++++++++++++++++++++
debian/rules | 16 ++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 22 +++++++++++++++++++
debian/watch | 1 +
9 files changed, 174 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..ace9831
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+inspect (0.0.20120109-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Tue, 29 Sep 2015 15:21:50 +0200
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..33477ea
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,55 @@
+Source: inspect
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: non-free/science
+XS-Autobuild: yes
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ libexpat1-dev,
+ zlib1g-dev,
+ python-all
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/inspect.git
+Vcs-Git: git://anonscm.debian.org/debian-med/inspect.git
+Homepage: http://proteomics.ucsd.edu/Software/Inspect/
+
+Package: inspect
+Architecture: any
+Depends: ${python:Depends},
+ ${misc:Depends}
+Description: mass-spectrometry database search tool
+ Inspect is a MS/MS database search tool specifically designed to address
+ two crucial needs of the proteomics comminuty: post-translational
+ modification identification and search speed. The program is available
+ as a free download or online in the ProteoSAFe webserver. The online
+ interface is coordinated with other proteomics software developed in the
+ lab, like PepNovo
+ .
+ Typical database searches do not deal well with the dynamic nature of
+ the proteome. Post-translational modifications, alternative splicing,
+ and laboratory chemisty all affect protein behavior and make spectrum
+ interpretation more challenging. The primary challenge is that the
+ "virtual database" of all modified peptides undergoes a combinatorial
+ explosion when a broad range of modifications is allowed. This affects
+ search running time. A secondary challenge is that in this richer
+ database, there are many more close "relatives" for each peptide. This
+ affects scoring accuracy, since differentiating between correct and
+ incorrect identifications is more difficult.
+ .
+ InsPecT addresses several algorithmic problems in order to identify
+ modified proteins.
+ .
+ InsPecT uses peptide sequence tags (PSTs) to filter the database.
+ InsPecT has an internal tag generator, but can accept tags generated by
+ other tools (e.g. Pepnovo, GutenTAG). Because de novo is imperfect,
+ multiple tags are produced for each spectrum, to ensure that (at least)
+ one tag is corrrect. These PSTs are extremely efficient filters, even in
+ the context of up to a dozen possible modifications. Tag-based filtering
+ can also be combined with the "two-pass" filtering pioneered by
+ X!Tandem, where from one search provides a list of proteins (a mini-
+ database) for a more detailed search.
+ .
+ Unanticipated modifications are common in proteomics. InsPecT implements
+ the MS-Alignment algorithm for "blind" spectral search, with no bias
+ toward anticipated modification types. This search has been applied to
+ annotate heavily-modified proteins such as crystallins.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..b0eb3f3
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,41 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: InsPecT
+Upstream-Contact: Natalie Castellana <ncastell at cs.ucsd.edu>
+Source: http://proteomics.ucsd.edu/Software/Inspect/Inspect.20120109.zip
+
+Files: *
+Copyright: 2005-2012 The Regents of the University of California
+ Stephen Tanner, Samuel Payne, Natalie Castellana, Pavel Pevzner, Vineet Bafna
+License: non-profit
+ Permission to use, copy, modify and distribute any part of this
+ program for educational, research and non-profit purposes, by non-profit
+ institutions only, without fee, and without a written agreement is hereby
+ granted, provided that the above copyright notice, this paragraph and
+ the following three paragraphs appear in all copies.
+ .
+ Those desiring to incorporate this work into commercial
+ products or use for commercial purposes should contact the Technology
+ Transfer & Intellectual Property Services, University of California,
+ San Diego, 9500 Gilman Drive, Mail Code 0910, La Jolla, CA 92093-0910,
+ Ph: (858) 534-5815, FAX: (858) 534-7345, E-MAIL:invent at ucsd.edu.
+ .
+ IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY
+ FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES,
+ INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN
+ IF THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY
+ OF SUCH DAMAGE.
+ .
+ THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE UNIVERSITY
+ OF CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES,
+ ENHANCEMENTS, OR MODIFICATIONS. THE UNIVERSITY OF CALIFORNIA MAKES NO
+ REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND, EITHER IMPLIED OR
+ EXPRESS, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT THE USE OF
+ THE SOFTWARE WILL NOT INFRINGE ANY PATENT, TRADEMARK OR OTHER RIGHTS.
+
+Files: debian/*
+Copyright: 2015 Andreas Tille <tille at debian.org>
+License: Apache-2.0
+ On Debian systems you can find the full text of the Apache License V2.0
+ at /usr/share/common-licenses/Apache-2.0
+
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..3d33173
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,32 @@
+#!/bin/sh
+# if you need to repack for whatever reason you can
+# use this script via uscan or directly
+#
+# FIXME: currently the code is not conform to Debian Policy
+# http://www.debian.org/doc/debian-policy/ch-source.html
+# "get-orig-source (optional)"
+# This target may be invoked in any directory, ...
+# --> currently it is assumed the script is called in the
+# source directory featuring the debian/ dir
+
+COMPRESS=xz
+
+set -e
+set -x
+NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
+dateversion=`echo $VERSION | sed 's/^0\.0\.//'`
+
+TARDIR=${NAME}-${VERSION}
+
+mkdir -p ../tarballs
+cd ../tarballs
+echo wget -q http://proteomics.ucsd.edu/Software/Inspect/Inspect.${dateversion}.zip
+
+mkdir ${TARDIR}
+cd ${TARDIR}
+unzip -q ../Inspect.${dateversion}.zip
+cd ..
+
+GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}"
+rm -rf ${TARDIR}
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..7b3c442
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,16 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+
+%:
+ dh $@ --with python2
+
+override_dh_install:
+ # due to name conflict with libboost-tools-dev we need to rename the binary
+ mkdir -p debian/$(DEBPKGNAME)/usr/bin
+ mv inspect debian/$(DEBPKGNAME)/usr/bin/ms-inspect
+
+get-orig-source:
+ sh debian/get-orig-source
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..8592cec
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,22 @@
+Reference:
+ - Author: Stephen Tanner and Hongjun Shu and Ari Frank and Ling-Chi Wang and Ebrahim Zandi and Marc Mumby and Pavel A. Pevzner and Vineet Bafna
+ Title: "InsPecT: Fast and accurate identification of post-translationally modified peptides from tandem mass spectra"
+ Journal: Anal Chem.
+ Year: 2005
+ Volume: 77
+ Number: 14
+ Pages: 4626-39
+ DOI: 10.1021/ac050102d
+ PMID: 16013882
+ URL: http://pubs.acs.org/doi/abs/10.1021/ac050102d
+ - Author: Ari Frank and Stephen Tanner and Vineet Bafna and Pavel Pevzner
+ Title: "Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry"
+ Journal: Journal of Proteome Research
+ Year: 2005
+ Volume: 4
+ Number: 4
+ Pages: 1287-95
+ DOI: 10.1021/pr050011x
+ PMID: 16083278
+ URL: http://pubs.acs.org/doi/abs/10.1021/pr050011x
+
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..d8ef91e
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1 @@
+# There is no tarball download location, this software is only available in SVN
--
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