[med-svn] r7207 - in trunk/packages/mgltools/cadd/trunk/debian: . patches source
Thorsten Alteholz
alteholz-guest at alioth.debian.org
Fri Jul 1 17:27:38 UTC 2011
Author: alteholz-guest
Date: 2011-07-01 17:27:38 +0000 (Fri, 01 Jul 2011)
New Revision: 7207
Added:
trunk/packages/mgltools/cadd/trunk/debian/manpages
trunk/packages/mgltools/cadd/trunk/debian/patches/
trunk/packages/mgltools/cadd/trunk/debian/patches/fix_shebangs.patch
trunk/packages/mgltools/cadd/trunk/debian/patches/series
trunk/packages/mgltools/cadd/trunk/debian/runCADD.1
trunk/packages/mgltools/cadd/trunk/debian/source/
trunk/packages/mgltools/cadd/trunk/debian/source/format
Removed:
trunk/packages/mgltools/cadd/trunk/debian/mgltools-cadd.lintian-overrides
Modified:
trunk/packages/mgltools/cadd/trunk/debian/control
trunk/packages/mgltools/cadd/trunk/debian/copyright
trunk/packages/mgltools/cadd/trunk/debian/rules
Log:
took care of lintian warnings and errors
Modified: trunk/packages/mgltools/cadd/trunk/debian/control
===================================================================
--- trunk/packages/mgltools/cadd/trunk/debian/control 2011-06-30 20:33:55 UTC (rev 7206)
+++ trunk/packages/mgltools/cadd/trunk/debian/control 2011-07-01 17:27:38 UTC (rev 7207)
@@ -17,10 +17,44 @@
Package: mgltools-cadd
XB-Python-Version: ${python:Versions}
Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}
-Description: XXX
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, mgltools-vision, mgltools-webservices
+Description: Computer Aided Drug Discovery (CADD) Pipeline
This package is part of the mgltools set of Python libraries which
provide an infrastructure for the analysis of protein structures and
their docking of chemical compounds.
.
- XXX
+ The Computer Aided Drug Discovery (CADD) Pipeline is a workflow environment
+ designed to support molecular dyanmics simulations and virtual screening
+ experiments for in silico drug discovery, with a special focus on supporting
+ the use of the Relaxed Complex Scheme. It includes web based access to
+ applications such as NAMD, AutoDock, PDB2PQR, APBS, MGLToos and couples them
+ in a flexible and scalable fashion through cloud computing.
+ It is developed as a standalone application, using Vision
+ (https://www.nbcr.net/pub/wiki/index.php?title=MGLTools#Vision)
+ as the backend engine for visual programming and workflow execution.
+ The scientific applications are made accessible through CADD using Opal Web
+ services (https://www.nbcr.net/pub/wiki/index.php?title=Opal) for scalable
+ and distributed computation.
+ .
+ The workflow components of the CADD pipeline are currently released as Vision
+ networks packaged for specific processes in a modular fashion. These modules
+ may be coupled at ease for more complex processes. In the future, they may
+ also be accessible from workflow repositories such as MyExperiment.org, and
+ from AutoDockTools.
+ The Opal services used in the CADD workflow may be accessed using programmatic
+ access, the Opal Server Dashboard or other workflow clients such as Kepler,
+ VisTrails or Taverna through Opal plugins available at Opal Sourceforge website
+ (http://opal.nbcr.net).
+ .
+ Features
+ .
+ * Automatic launching of NAMD simulation on TeraGrid and NBCR resources,
+ including experimental support for migration of simulation between
+ resources.
+ * Selection of representative snapshots/conformations from MD simulations
+ using clustering tools such as QR factorization from VMD and Ptraj from
+ Amber.
+ * Support of Virtual Screening using AutoDock, AutoDock Vina
+ * Support of Relaxed Complex Scheme based Virtual Screening and Rescoring
+ * Visualization and analysis of Virtual Screening hits
+
Modified: trunk/packages/mgltools/cadd/trunk/debian/copyright
===================================================================
--- trunk/packages/mgltools/cadd/trunk/debian/copyright 2011-06-30 20:33:55 UTC (rev 7206)
+++ trunk/packages/mgltools/cadd/trunk/debian/copyright 2011-07-01 17:27:38 UTC (rev 7207)
@@ -1,5 +1,5 @@
-This package was debianized by Steffen Moeller <moeller at debian.org> on
-Thu, 10 Jul 2008 00:03:24 +0200
+This package was debianized by Thorsten Alteholz <debian at alteholz.de> on
+Fri, 01 Jul 2011 18:00:00 +0200
It was downloaded from http://mgltools.scripps.edu
@@ -21,11 +21,22 @@
Guillaume Vareille <vareille at scripps.edu>
Daniel Stoffler <stoffler at scripps.edu>
Michael F. Sanner <sanner at scripps.edu>
+ Sargis Dallakyan (TSRI)
+ Stefano Forli (TSRI)
+ Ruth Huey (TSRI)
+ Art Olson (TSRI)
+ Nadya Williams (UCSD)
+ Wilfred Li (UCSD)
+ Andy McCammon (UCSD)
+ Jane Ren (UCSD)
+ Rommie Amarao (UCI)
+ Luca Clementi (alumni)
+ Guillaume Vareille (alumni)
Copyright:
The respective authors and the Scripps Research Institute
- Copyright 1989-2008 Michael Sanner <sanner at scripps.edu>
+ Copyright 1989-2011 Michael Sanner <sanner at scripps.edu>
License:
@@ -78,6 +89,5 @@
NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR
MODIFICATIONS.
-The Debian packaging is Copyright (C) 2007-2008,
-Steffen Moeller <moeller at debian.org>
+The Debian packaging is Copyright (C) 2011, Thorsten Alteholz <debian at alteholz.de>
and is licensed under the GPL, see '/usr/share/common-licenses/GPL'.
Added: trunk/packages/mgltools/cadd/trunk/debian/manpages
===================================================================
--- trunk/packages/mgltools/cadd/trunk/debian/manpages (rev 0)
+++ trunk/packages/mgltools/cadd/trunk/debian/manpages 2011-07-01 17:27:38 UTC (rev 7207)
@@ -0,0 +1 @@
+debian/runCADD.1
Deleted: trunk/packages/mgltools/cadd/trunk/debian/mgltools-cadd.lintian-overrides
===================================================================
--- trunk/packages/mgltools/cadd/trunk/debian/mgltools-cadd.lintian-overrides 2011-06-30 20:33:55 UTC (rev 7206)
+++ trunk/packages/mgltools/cadd/trunk/debian/mgltools-cadd.lintian-overrides 2011-07-01 17:27:38 UTC (rev 7207)
@@ -1,2 +0,0 @@
-# the license is in debian/copyright but upstream wants to have it there as well
-mgltools-cadd: extra-license-file
Added: trunk/packages/mgltools/cadd/trunk/debian/patches/fix_shebangs.patch
===================================================================
--- trunk/packages/mgltools/cadd/trunk/debian/patches/fix_shebangs.patch (rev 0)
+++ trunk/packages/mgltools/cadd/trunk/debian/patches/fix_shebangs.patch 2011-07-01 17:27:38 UTC (rev 7207)
@@ -0,0 +1,37 @@
+Description: drop hardcoded python2.x dependency
+Author: Thorsten Alteholz <debian at alteholz.de>
+Last-Update: 2011-07-01
+Index: mgltools-cadd-1.5.6/CADD/bin/runCADD
+===================================================================
+--- mgltools-cadd-1.5.6.org/CADD/bin/runCADD 2011-07-01 18:08:33.000000000 +0200
++++ mgltools-cadd-1.5.6/CADD/bin/runCADD 2011-07-01 18:09:21.000000000 +0200
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python2.4
++#!/usr/bin/python
+ # $Header: /opt/cvs/CADD/bin/runCADD,v 1.2 2011/01/18 00:56:07 nadya Exp $
+ # $Id: runCADD,v 1.2 2011/01/18 00:56:07 nadya Exp $
+
+Index: mgltools-cadd-1.5.6/CADD/bin/CADD
+===================================================================
+--- mgltools-cadd-1.5.6.org/CADD/bin/CADD 2011-07-01 18:08:38.000000000 +0200
++++ mgltools-cadd-1.5.6/CADD/bin/CADD 2011-07-01 18:09:47.000000000 +0200
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python2.5
++#!/usr/bin/env python
+ #
+ # $Header: /opt/cvs/CADD/bin/CADD,v 1.2 2011/01/18 00:56:07 nadya Exp $
+ # $Id: CADD,v 1.2 2011/01/18 00:56:07 nadya Exp $
+
+Index: mgltools-cadd-1.5.6/setup.py
+===================================================================
+--- mgltools-cadd-1.5.6.org/setup.py 2011-07-01 18:24:45.000000000 +0200
++++ mgltools-cadd-1.5.6/setup.py 2011-07-01 18:25:10.000000000 +0200
+@@ -43,7 +43,7 @@
+ forig = open(script+".py", "r")
+ txt = forig.readlines()
+ forig.close()
+- fnew.write("#!/usr/bin/env python2.5\n")
++ fnew.write("#!/usr/bin/env python\n")
+ fnew.writelines(txt)
+ fnew.close()
+ build_scripts.copy_scripts(self)
Added: trunk/packages/mgltools/cadd/trunk/debian/patches/series
===================================================================
--- trunk/packages/mgltools/cadd/trunk/debian/patches/series (rev 0)
+++ trunk/packages/mgltools/cadd/trunk/debian/patches/series 2011-07-01 17:27:38 UTC (rev 7207)
@@ -0,0 +1 @@
+fix_shebangs.patch
Modified: trunk/packages/mgltools/cadd/trunk/debian/rules
===================================================================
--- trunk/packages/mgltools/cadd/trunk/debian/rules 2011-06-30 20:33:55 UTC (rev 7206)
+++ trunk/packages/mgltools/cadd/trunk/debian/rules 2011-07-01 17:27:38 UTC (rev 7207)
@@ -12,5 +12,11 @@
%:
dh $@ --with python2
+override_dh_install:
+ find . -name runCADD -exec cat {} \;
+ dh_install
+ find . -name runCADD -exec chmod 755 {} \;
+ find . -name *.prm -o -name *.res | xargs -r chmod -x
+
get-orig-source:
./debian/get-orig-source/get-orig-source $(SRC) $(BRANCH) $(RCVERSION)
Added: trunk/packages/mgltools/cadd/trunk/debian/runCADD.1
===================================================================
--- trunk/packages/mgltools/cadd/trunk/debian/runCADD.1 (rev 0)
+++ trunk/packages/mgltools/cadd/trunk/debian/runCADD.1 2011-07-01 17:27:38 UTC (rev 7207)
@@ -0,0 +1,85 @@
+.\" 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 CADD 1 "July 1, 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
+CADD \- A computer aided drug design using Vision
+.SH SYNOPSIS
+.B runCADD
+.RI [ options ]
+.RI [ filenames ]
+
+.SH DESCRIPTION
+This manual page is an almost literal translation of the output
+provided by
+.B runCADD -h
+command.
+.PP
+.\" TeX users may be more comfortable with the \fB<whatever>\fP and
+.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
+.\" respectively.
+.SH OPTIONS
+A summary of options is included below.
+For a complete description, refer to the tutorials and documentation
+that is available online.
+
+Files <filenames> ending in "net.py" will be laoded as networks in vision.
+Other files will be executed as Python scripts in which "ed" refers
+to the VisualProgrammingEnvironment instance.
+
+.TP
+.B \-h, \-\-help
+Show summary of options.
+.TP
+.B \-e, \-\-runAndExit
+run the networks and exit
+.TP
+.B \-p, \-\-ipython
+create an ipython shell instead of a python shell
+.TP
+.B \-r, \-\-run
+run the networks on the command line
+.TP
+.B \-s, \-\-noSplash
+doesn't show the CADD splash screen (works only if registered)
+.TP
+.B \-t, \-\-NoTerminal
+vision provides its own shell (under menu 'Edit') instead of the terminal
+.TP
+.B \-\-resourceFolder foldername
+stores resource file under .name (defaults to .mgltools)
+
+.TP
+port values can be passed on the command line (but not to macros):
+ Network_net.py nodeName:portName:value
+
+.\".SH EXAMPLE:
+.\"display protein as ribbon, non protein as sticks and balls
+.\"and color by atom type
+.\".TP
+.\"pmv \-i \-\-dmode sssb \-\-cmode cr myprot.pdb
+.\".TP
+.\"pmv \-i \-m sssb \-c cr myprot.pdb
+
+
+.SH SEE ALSO
+.BR http://mgltools.scripps.edu
+.SH AUTHOR
+runCADD was written by researchers of the Molecular
+Graphics Lab at the Scripps Institute <mgltools at scripps.edu>.
+.PP
+This manual page was written by Thorsten Alteholz <debian at alteholz.de>,
+for the Debian project (but may be used by others).
Added: trunk/packages/mgltools/cadd/trunk/debian/source/format
===================================================================
--- trunk/packages/mgltools/cadd/trunk/debian/source/format (rev 0)
+++ trunk/packages/mgltools/cadd/trunk/debian/source/format 2011-07-01 17:27:38 UTC (rev 7207)
@@ -0,0 +1 @@
+3.0 (quilt)
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