[med-svn] r7219 - in trunk/packages: . raccoon raccoon/trunk raccoon/trunk/debian raccoon/trunk/debian/patches raccoon/trunk/debian/source
Steffen Möller
moeller at alioth.debian.org
Mon Jul 4 22:55:39 UTC 2011
Author: moeller
Date: 2011-07-04 22:55:39 +0000 (Mon, 04 Jul 2011)
New Revision: 7219
Added:
trunk/packages/raccoon/
trunk/packages/raccoon/trunk/
trunk/packages/raccoon/trunk/debian/
trunk/packages/raccoon/trunk/debian/README.Debian
trunk/packages/raccoon/trunk/debian/README.source
trunk/packages/raccoon/trunk/debian/changelog
trunk/packages/raccoon/trunk/debian/compat
trunk/packages/raccoon/trunk/debian/control
trunk/packages/raccoon/trunk/debian/copyright
trunk/packages/raccoon/trunk/debian/manpages
trunk/packages/raccoon/trunk/debian/menu
trunk/packages/raccoon/trunk/debian/patches/
trunk/packages/raccoon/trunk/debian/patches/python_path.patch
trunk/packages/raccoon/trunk/debian/patches/series
trunk/packages/raccoon/trunk/debian/patches/syntaxError_columnspan.patch
trunk/packages/raccoon/trunk/debian/raccoon.1
trunk/packages/raccoon/trunk/debian/raccoon.dirs
trunk/packages/raccoon/trunk/debian/rules
trunk/packages/raccoon/trunk/debian/source/
trunk/packages/raccoon/trunk/debian/source/format
trunk/packages/raccoon/trunk/debian/watch
Log:
Prepared package for 'raccoon', a tool to orchestrate larger
drug screening projects.
Property changes on: trunk/packages/raccoon/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/raccoon/trunk/debian/README.Debian
===================================================================
--- trunk/packages/raccoon/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/raccoon/trunk/debian/README.Debian 2011-07-04 22:55:39 UTC (rev 7219)
@@ -0,0 +1,18 @@
+raccoon for Debian
+------------------
+
+This package interlinks
+
+ chemical ligand databases
+ protein structure databases
+
+and the tools for ligand docking
+
+ autodock, autodock-vina
+ their preparation environment MGLTools
+
+so that a complete project can be performed that investigates many thousands
+of ligands against a single or multiple structures, demanding compute times
+of many years.
+
+ -- Steffen Moeller <moeller at debian.org> Sun, 19 Jun 2011 13:20:27 +0200
Added: trunk/packages/raccoon/trunk/debian/README.source
===================================================================
--- trunk/packages/raccoon/trunk/debian/README.source (rev 0)
+++ trunk/packages/raccoon/trunk/debian/README.source 2011-07-04 22:55:39 UTC (rev 7219)
@@ -0,0 +1,9 @@
+raccoon for Debian
+------------------
+
+The downloaded .tar.gz was unpacked and the single
+file moved into a subdirectory to fit the Debian
+packagename-version principle. Subsequent taring
+for the packagename_version.orig.tar.gz was performed
+with GZIP=-9n flags.
+
Added: trunk/packages/raccoon/trunk/debian/changelog
===================================================================
--- trunk/packages/raccoon/trunk/debian/changelog (rev 0)
+++ trunk/packages/raccoon/trunk/debian/changelog 2011-07-04 22:55:39 UTC (rev 7219)
@@ -0,0 +1,5 @@
+raccoon (1.0-1) unstable; urgency=low
+
+ * Initial release (Closes: #630977)
+
+ -- Steffen Moeller <moeller at debian.org> Sun, 19 Jun 2011 13:20:27 +0200
Added: trunk/packages/raccoon/trunk/debian/compat
===================================================================
--- trunk/packages/raccoon/trunk/debian/compat (rev 0)
+++ trunk/packages/raccoon/trunk/debian/compat 2011-07-04 22:55:39 UTC (rev 7219)
@@ -0,0 +1 @@
+8
Added: trunk/packages/raccoon/trunk/debian/control
===================================================================
--- trunk/packages/raccoon/trunk/debian/control (rev 0)
+++ trunk/packages/raccoon/trunk/debian/control 2011-07-04 22:55:39 UTC (rev 7219)
@@ -0,0 +1,33 @@
+Source: raccoon
+Section: contrib/science
+Priority: extra
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 8.0.0)
+Standards-Version: 3.9.2
+Homepage: http://autodock.scripps.edu/resources/raccoon
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/raccoon/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/raccoon/trunk/
+
+Package: raccoon
+Architecture: all
+Depends: ${misc:Depends}, python, autodocktools
+Suggests: autodock, autodock-vina, torque
+Description: preparation of in silico drug screening projects
+ The field of computational biology is all about modeling
+ physiochemical entities. Structural biology is about how
+ those entities look in 3D and behave. And we have a drug
+ when we can change that behaviour in a way that we want it
+ to be changed - and only that behaviour.
+ .
+ Some good part of the characterisation of promising
+ drug-like compounds for their interaction with a larger protein
+ can be done on computers. This package helps with getting
+ collections of small ligands prepared to be fitted against
+ a particular protein of known structure. That docking itself
+ is then to be performed by autodock or autodock-vina.
+ .
+ Raccoon may not find the drug, but it may well find a
+ lead to it. To have this package with Debian shall help
+ smaller biochemistry labs and grants an opportunity for the
+ general public to educate itself and/or actively join in to
+ help the world .... just a bit.
Added: trunk/packages/raccoon/trunk/debian/copyright
===================================================================
--- trunk/packages/raccoon/trunk/debian/copyright (rev 0)
+++ trunk/packages/raccoon/trunk/debian/copyright 2011-07-04 22:55:39 UTC (rev 7219)
@@ -0,0 +1,31 @@
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: raccoon
+Source: http://autodock.scripps.edu/resources/raccoon
+
+Files: *
+Copyright: 2009 Stefano Forli <forli at scipps.edu>
+ Molecular Graphics Lab
+ The Scripps Research Institute
+License: GPL-3.0+
+
+Files: debian/*
+Copyright: 2011 Steffen Moeller <moeller at debian.org>
+License: GPL-3.0+
+
+License: GPL-3.0+
+ This program 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 3 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 3 can be found in "/usr/share/common-licenses/GPL-3".
+
Added: trunk/packages/raccoon/trunk/debian/manpages
===================================================================
--- trunk/packages/raccoon/trunk/debian/manpages (rev 0)
+++ trunk/packages/raccoon/trunk/debian/manpages 2011-07-04 22:55:39 UTC (rev 7219)
@@ -0,0 +1 @@
+debian/raccoon.1
Added: trunk/packages/raccoon/trunk/debian/menu
===================================================================
--- trunk/packages/raccoon/trunk/debian/menu (rev 0)
+++ trunk/packages/raccoon/trunk/debian/menu 2011-07-04 22:55:39 UTC (rev 7219)
@@ -0,0 +1,2 @@
+?package(raccoon):needs="X11" section="Applications/Science/Chemistry"\
+ title="raccoon" command="/usr/bin/raccoon"
Added: trunk/packages/raccoon/trunk/debian/patches/python_path.patch
===================================================================
--- trunk/packages/raccoon/trunk/debian/patches/python_path.patch (rev 0)
+++ trunk/packages/raccoon/trunk/debian/patches/python_path.patch 2011-07-04 22:55:39 UTC (rev 7219)
@@ -0,0 +1,10 @@
+Index: raccoon-1.0/raccoon.py
+===================================================================
+--- raccoon-1.0.orig/raccoon.py 2011-06-19 13:41:21.226381461 +0200
++++ raccoon-1.0/raccoon.py 2011-06-19 13:41:30.234426129 +0200
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python
+ #
+ # Raccoon
+ #
Added: trunk/packages/raccoon/trunk/debian/patches/series
===================================================================
--- trunk/packages/raccoon/trunk/debian/patches/series (rev 0)
+++ trunk/packages/raccoon/trunk/debian/patches/series 2011-07-04 22:55:39 UTC (rev 7219)
@@ -0,0 +1,2 @@
+syntaxError_columnspan.patch
+python_path.patch
Added: trunk/packages/raccoon/trunk/debian/patches/syntaxError_columnspan.patch
===================================================================
--- trunk/packages/raccoon/trunk/debian/patches/syntaxError_columnspan.patch (rev 0)
+++ trunk/packages/raccoon/trunk/debian/patches/syntaxError_columnspan.patch 2011-07-04 22:55:39 UTC (rev 7219)
@@ -0,0 +1,13 @@
+Index: raccoon-1.0/raccoon.py
+===================================================================
+--- raccoon-1.0.orig/raccoon.py 2011-06-19 13:39:11.101736203 +0200
++++ raccoon-1.0/raccoon.py 2011-06-19 13:42:35.202748288 +0200
+@@ -5610,7 +5610,7 @@
+ OutputDirLabel = Label(Summary_group.interior(), textvariable = JobDirectory, justify = LEFT)
+ OutputDirLabel.grid(row = 5, column = 2, padx = 5, sticky = W)
+ OutputDirLabelInfo = Label(Summary_group.interior(), textvariable = JobDirectoryInfo)
+-OutputDirLabelInfo.grid(row = 6, column = 1, columnspan = 3, padx = 5, sticky = S, columnspan = 2)
++OutputDirLabelInfo.grid(row = 6, column = 1, columnspan = 2, padx = 5, sticky = S)
+
+ JobsSummaryLabel = Label(Summary_group.interior(), textvariable = JobsSummary)
+ JobsSummaryLabel.grid(row = 7, column = 1, columnspan = 2, padx = 5, sticky = S)
Added: trunk/packages/raccoon/trunk/debian/raccoon.1
===================================================================
--- trunk/packages/raccoon/trunk/debian/raccoon.1 (rev 0)
+++ trunk/packages/raccoon/trunk/debian/raccoon.1 2011-07-04 22:55:39 UTC (rev 7219)
@@ -0,0 +1,36 @@
+.\" Hey, EMACS: -*- nroff -*-
+.\" First parameter, NAME, should be all caps
+.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
+.\" other parameters are allowed: see man(7), man(1)
+.TH RACCOON 1 "June 19, 2011"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+raccoon \- preparation of ligand screening projects
+.SH SYNOPSIS
+.B raccoon
+.SH DESCRIPTION
+\fBraccoon\fP takes a ligand library and the crystal structure of a protein,
+forms many small jobs to investigate the energy gained by bringing the two
+together, and allows the submission of such jobs to a job queuing engine.
+.SH SEE ALSO
+.BR autodock (1),
+.BR autogrid (1).
+.br
+The programs are documented fully on the home page
+.IR "http://autodock.scripps.edu/resources/raccoon" ,
+.SH AUTHOR
+raccoon was written by Stefano Forli from The Scripps Institute.
+.PP
+This manual page was written by Steffen Moeller <moeller at debian.org>,
+for the Debian project (and may be used by others).
Added: trunk/packages/raccoon/trunk/debian/raccoon.dirs
===================================================================
--- trunk/packages/raccoon/trunk/debian/raccoon.dirs (rev 0)
+++ trunk/packages/raccoon/trunk/debian/raccoon.dirs 2011-07-04 22:55:39 UTC (rev 7219)
@@ -0,0 +1 @@
+usr/bin
Added: trunk/packages/raccoon/trunk/debian/rules
===================================================================
--- trunk/packages/raccoon/trunk/debian/rules (rev 0)
+++ trunk/packages/raccoon/trunk/debian/rules 2011-07-04 22:55:39 UTC (rev 7219)
@@ -0,0 +1,18 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@
+
+override_dh_autobuild:
+
+override_dh_install:
+ cp raccoon.py $(CURDIR)/debian/raccoon/usr/bin/raccoon
Property changes on: trunk/packages/raccoon/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/raccoon/trunk/debian/source/format
===================================================================
--- trunk/packages/raccoon/trunk/debian/source/format (rev 0)
+++ trunk/packages/raccoon/trunk/debian/source/format 2011-07-04 22:55:39 UTC (rev 7219)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/raccoon/trunk/debian/watch
===================================================================
--- trunk/packages/raccoon/trunk/debian/watch (rev 0)
+++ trunk/packages/raccoon/trunk/debian/watch 2011-07-04 22:55:39 UTC (rev 7219)
@@ -0,0 +1,2 @@
+version=3
+http://mgldev.scripps.edu/raccoon/raccoon-([0-9.]+)tar\.gz
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