[med-svn] r7662 - trunk/packages/autodocksuite/trunk/debian
Steffen Möller
moeller at alioth.debian.org
Sun Sep 4 18:48:48 UTC 2011
Author: moeller
Date: 2011-09-04 18:48:48 +0000 (Sun, 04 Sep 2011)
New Revision: 7662
Added:
trunk/packages/autodocksuite/trunk/debian/autodock-getdata.README.Debian
trunk/packages/autodocksuite/trunk/debian/autodock-getdata.install
trunk/packages/autodocksuite/trunk/debian/autodock-getdata.upstream-metadata.yaml
trunk/packages/autodocksuite/trunk/debian/autodock-zinc.getData
trunk/packages/autodocksuite/trunk/debian/autodock.upstream-metadata.yaml
Removed:
trunk/packages/autodocksuite/trunk/debian/upstream-metadata.yaml
Modified:
trunk/packages/autodocksuite/trunk/debian/README.Debian
trunk/packages/autodocksuite/trunk/debian/changelog
trunk/packages/autodocksuite/trunk/debian/control
trunk/packages/autodocksuite/trunk/debian/rules
Log:
Linked autodock with getData.
Modified: trunk/packages/autodocksuite/trunk/debian/README.Debian
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/README.Debian 2011-09-04 18:47:24 UTC (rev 7661)
+++ trunk/packages/autodocksuite/trunk/debian/README.Debian 2011-09-04 18:48:48 UTC (rev 7662)
@@ -37,6 +37,4 @@
improving the AutoDock/-Grid packaging for Debian also go to David
Paleino and the Debian-Med community at large.
-Steffen
-
-- Steffen Moeller <moeller at debian.org> Mon, 15 Dec 2008 01:01:37 +0100
Added: trunk/packages/autodocksuite/trunk/debian/autodock-getdata.README.Debian
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/autodock-getdata.README.Debian (rev 0)
+++ trunk/packages/autodocksuite/trunk/debian/autodock-getdata.README.Debian 2011-09-04 18:48:48 UTC (rev 7662)
@@ -0,0 +1,14 @@
+autodock-getdata
+================
+
+The integration of 'getData' with Debian is still in its infancy.
+We will be learning while we are doing it.
+
+The PDBQT-variant of mol2 files in ZINC is described in
+November 2, 2009 volume 8 of the FightAids at Home newletter,
+available online on
+ http://fightaidsathome.scripps.edu/images/FAAHvol8.pdf
+Files can be retrieved manually on
+ http://zinc.docking.org/pdbqt/
+
+-- Steffen Moeller <moeller at debian.org> Sun, 04 Sep 2011 00:51:12 +0200
Added: trunk/packages/autodocksuite/trunk/debian/autodock-getdata.install
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/autodock-getdata.install (rev 0)
+++ trunk/packages/autodocksuite/trunk/debian/autodock-getdata.install 2011-09-04 18:48:48 UTC (rev 7662)
@@ -0,0 +1 @@
+debian/autodock-zinc.getData /etc/getData.conf.d/
Copied: trunk/packages/autodocksuite/trunk/debian/autodock-getdata.upstream-metadata.yaml (from rev 7631, trunk/packages/autodocksuite/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/autodock-getdata.upstream-metadata.yaml (rev 0)
+++ trunk/packages/autodocksuite/trunk/debian/autodock-getdata.upstream-metadata.yaml 2011-09-04 18:48:48 UTC (rev 7662)
@@ -0,0 +1,13 @@
+DOI: 10.1021/ci049714
+Homepage: http://zinc.docking.org
+Name: ZINC
+PMID: 15667143
+Reference:
+ Author: John J. Irwin and Brian K. Shoichet
+ Title: ZINC – A Free Database of Commercially Available Compounds for Virtual Screening
+ Journal: J Chem Inf Model.
+ Volume: 45
+ Number: 1
+ Pages: 177-182
+ Year: 2005
+ URL: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1360656/
Added: trunk/packages/autodocksuite/trunk/debian/autodock-zinc.getData
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/autodock-zinc.getData (rev 0)
+++ trunk/packages/autodocksuite/trunk/debian/autodock-zinc.getData 2011-09-04 18:48:48 UTC (rev 7662)
@@ -0,0 +1,24 @@
+print STDERR "Reading autodock-zinc configuration file\n" if $verbose;
+
+# This file is Copyright (C) Steffen Moeller <moeller at debian.org>
+# and made availabel under the terms of the GPL version 2 or any
+# later version as presented in '/usr/share/common-licenses/GPL-2'.
+
+# No chemical post-processing required since all files are in pdbqt format
+# already. But one needs to untar the files.
+
+foreach $n (("asinex", "chembridge_buildingblocks_pdbqt_1000split", "drugbank_nutraceutics",
+ "drugbank_smallmol", "fda_approved", "human_metabolome_pdbqt_1000split", "otava",
+ "zinc_natural_products")) {
+
+ print "$n\n";
+
+ $toBeMirrored{"zinc.pdbqt.$n"}={
+ "name" => "ZINC - PDBQT formatted – $n",
+ "tags" => ["pdbqt","compounds"],
+ "source" => "wget $sharedWgetOptions http://zinc.docking.org/pdbqt/$n.tar.gz",
+ "post-download" => "tar --no-same-owner --exclude prepare_lig.log --exclude mol2 -xzvf $n.tar.gz && chmod -R go+r . && find . -type d -exec chmod +x {} \\; "
+ };
+}
+
+1;
Copied: trunk/packages/autodocksuite/trunk/debian/autodock.upstream-metadata.yaml (from rev 7631, trunk/packages/autodocksuite/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/autodock.upstream-metadata.yaml (rev 0)
+++ trunk/packages/autodocksuite/trunk/debian/autodock.upstream-metadata.yaml 2011-09-04 18:48:48 UTC (rev 7662)
@@ -0,0 +1,18 @@
+Donation: http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/
+DOI: 10.1002/jcc.21256
+Homepage: http://autodock.scripps.edu/
+Name: AutoDock
+PMID: 19399780
+Reference:
+ Author: Garrett M. Morris, Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell and Arthur J. Olson.
+ Title: AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
+ Journal: Journal of Computational Chemistry
+ Volume: 30
+ Number: 16
+ Pages: 2785-2791
+ Year: 2009
+ URL: http://www3.interscience.wiley.com/journal/122365050/abstract
+Registration: http://autodock.scripps.edu/downloads/autodock-registration
+Watch: |
+ opts="dversionmangle=s/\+rc/~rc/" \
+ http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/ \.\./autodock-registration/tars/.*/autodocksuite-(.*)-src\.tar\.gz
Modified: trunk/packages/autodocksuite/trunk/debian/changelog
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/changelog 2011-09-04 18:47:24 UTC (rev 7661)
+++ trunk/packages/autodocksuite/trunk/debian/changelog 2011-09-04 18:48:48 UTC (rev 7662)
@@ -1,3 +1,12 @@
+autodocksuite (4.2.3-2) unstable; urgency=low
+
+ * Recompilation with gcc-4.6
+ * Yet no link time optimisation because of compiler errors
+ * Added package with download instructions for getData
+ * Rendering debian/rules more sensitive to build errors
+
+ -- Steffen Moeller <moeller at debian.org> Sun, 04 Sep 2011 00:01:02 +0200
+
autodocksuite (4.2.3-1) unstable; urgency=low
* New upstream version.
Modified: trunk/packages/autodocksuite/trunk/debian/control
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/control 2011-09-04 18:47:24 UTC (rev 7661)
+++ trunk/packages/autodocksuite/trunk/debian/control 2011-09-04 18:48:48 UTC (rev 7662)
@@ -6,8 +6,8 @@
Charles Plessy <plessy at debian.org>, Nelson A. de Oliveira <naoliv at debian.org>,
Andreas Tille <tille at debian.org>
Build-Depends: debhelper (>= 7), automake, csh
-Standards-Version: 3.8.4
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/autodocksuite/trunk/?rev=0&sc=0
+Standards-Version: 3.9.2
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/autodocksuite/trunk/
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/autodocksuite/trunk/
Homepage: http://autodock.scripps.edu/
@@ -54,3 +54,30 @@
Depends: ${misc:Depends}
Description: test files for AutoGrid
This package contain the test files for the AutoGrid program.
+
+Package: autodock-getdata
+Architecture: all
+Suggests: autodock, autogrid, autodocktools
+Recommends: getdata
+Depends: ${misc:Depends}
+Description: instructions for getData to collect compounds
+ This package provides instructions for getData to retrieve
+ descriptions for sets of molecular compounds that can be used
+ directly as input for autodock. The data is not provided
+ direclty by this package. Only the instructions for the download
+ are maintained here.
+ .
+ The FightAids at Home project of the World Community Grid publicly
+ provides the input sets of their runs. The original structures
+ come from the ZINC database and have been processed from the
+ mol2 to pdbqt format by the Scripps institute:
+ * asinex
+ * chembridge_buildingblocks_pdbqt_1000split
+ * drugbank_nutraceutics
+ * drugbank_smallmol
+ * fda_approved
+ * human_metabolome_pdbqt_1000split
+ * otava
+ * zinc_natural_products
+ .
+ Please cite the ZINC database when using that data.
Modified: trunk/packages/autodocksuite/trunk/debian/rules
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/rules 2011-09-04 18:47:24 UTC (rev 7661)
+++ trunk/packages/autodocksuite/trunk/debian/rules 2011-09-04 18:48:48 UTC (rev 7662)
@@ -4,6 +4,13 @@
#export DH_VERBOSE=1
export DH_OPTIONS
+SHELL := /bin/bash
+
+#CXX=g++
+#CC=gcc
+CXX=/usr/lib/gcc-snapshot/bin/g++
+CC=/usr/lib/gcc-snapshot/bin/gcc
+
# see http://www.gentoo.org/proj/en/qa/asneeded.xml
LDFLAGS="-Wl,--as-needed"
@@ -19,7 +26,7 @@
CFLAGS += -O2
endif
-CFLAGS=-Winline -finline-functions
+CFLAGS += -Winline -finline-functions
# the suggested const is not working sufficiently, for gcc-4.6 and higher
#CFLAGS += -Wsuggest-attribute=const
@@ -29,8 +36,9 @@
configure: configure-stamp
configure-stamp: $(QUILT_STAMPFN)
dh_testdir
+ set -e; \
for d in autogrid autodock; do \
- ( cd $$d && autoreconf -i && ./configure LDFLAGS="$(LDFLAGS)" CFLAGS="$(CFLAGS)" CXXFLAGS="$(CXXFLAGS)" --prefix=/usr ) \
+ ( cd $$d && autoreconf -i && ./configure CC="$(CC)" CXX="$(CXX)" LDFLAGS="$(LDFLAGS)" CFLAGS="$(CFLAGS)" CXXFLAGS="$(CXXFLAGS)" --prefix=/usr ) \
done
touch configure-stamp
@@ -39,6 +47,7 @@
build-arch: build-arch-stamp
build-arch-stamp: configure-stamp
+ set -e; \
for d in autogrid autodock; do $(MAKE) -C $$d; done
touch $@
@@ -51,7 +60,6 @@
dh_testdir
dh_testroot
rm -f build-arch-stamp build-indep-stamp configure-stamp
-
for d in autodock autogrid; \
do \
if [ -r $$d/Makefile ]; then $(MAKE) -C $$d distclean; fi \
Deleted: trunk/packages/autodocksuite/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/upstream-metadata.yaml 2011-09-04 18:47:24 UTC (rev 7661)
+++ trunk/packages/autodocksuite/trunk/debian/upstream-metadata.yaml 2011-09-04 18:48:48 UTC (rev 7662)
@@ -1,18 +0,0 @@
-Donation: http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/
-DOI: 10.1002/jcc.21256
-Homepage: http://autodock.scripps.edu/
-Name: AutoDock
-PMID: 19399780
-Reference:
- Author: Garrett M. Morris, Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell and Arthur J. Olson.
- Title: AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
- Journal: Journal of Computational Chemistry
- Volume: 30
- Number: 16
- Pages: 2785-2791
- Year: 2009
- URL: http://www3.interscience.wiley.com/journal/122365050/abstract
-Registration: http://autodock.scripps.edu/downloads/autodock-registration
-Watch: |
- opts="dversionmangle=s/\+rc/~rc/" \
- http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/ \.\./autodock-registration/tars/.*/autodocksuite-(.*)-src\.tar\.gz
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