[med-svn] r1129 - in trunk/packages/mustang/trunk/debian: . patches
mok0-guest at alioth.debian.org
mok0-guest at alioth.debian.org
Sun Jan 13 22:20:18 UTC 2008
Author: mok0-guest
Date: 2008-01-13 22:20:17 +0000 (Sun, 13 Jan 2008)
New Revision: 1129
Added:
trunk/packages/mustang/trunk/debian/test_zf-CCHH-small
Modified:
trunk/packages/mustang/trunk/debian/changelog
trunk/packages/mustang/trunk/debian/control
trunk/packages/mustang/trunk/debian/copyright
trunk/packages/mustang/trunk/debian/patches/test_zf-cchh.dpatch
trunk/packages/mustang/trunk/debian/rules
trunk/packages/mustang/trunk/debian/runtest
Log:
Upstream tarball no longer needs to be repackaged. License issues with PDB files are
now clarified. It is legal to distribute the PDB file present in upstream tarball.
- PDB advisory text included in debian/copyright
- To keep size of package down, the test data is provided in a separate, indep-arch
package. The test data can thus be installed and uninstalled independent of the
mustang program itself.
- debian/rules modified to build binary and indep packages.
- Package no longer needs to be named with the dfsg tag.
Modified: trunk/packages/mustang/trunk/debian/changelog
===================================================================
--- trunk/packages/mustang/trunk/debian/changelog 2008-01-12 16:07:22 UTC (rev 1128)
+++ trunk/packages/mustang/trunk/debian/changelog 2008-01-13 22:20:17 UTC (rev 1129)
@@ -1,11 +1,12 @@
-mustang (3.0.dfsg-1) unstable; urgency=low
+mustang (3.0-1) unstable; urgency=low
[ Morten Kjeldgaard ]
* Upload mustang to Debian (Closes: #459637).
* debian/control: Maintainer and homepage fields set as per
Debian policy.
+ * Include test pdb files in a separate package.
* debian/rules: add get-orig-source target.
-
+
[ Andreas Tille ]
* Maintainer: Debian-Med Packaging Team
Uploaders: Morten Kjeldgaard <mok at bioxray.dk>
Modified: trunk/packages/mustang/trunk/debian/control
===================================================================
--- trunk/packages/mustang/trunk/debian/control 2008-01-12 16:07:22 UTC (rev 1128)
+++ trunk/packages/mustang/trunk/debian/control 2008-01-13 22:20:17 UTC (rev 1129)
@@ -20,3 +20,17 @@
Based on a progressive pairwise heuristic the algorithm then proceeds
through a number of refinement passes. Mustang reports the multiple
sequence alignment and the corresponding superposition of structures.
+
+Package: mustang-testdata
+Architecture: all
+Enhances: mustang
+Description: multiple structural alignment of proteins, test data
+ Mustang is an algorithm for structural alignment of multiple
+ protein structures. Given a set of PDB files, the program uses the spatial
+ information in the Calpha atoms of the set to produce a sequence alignment.
+ Based on a progressive pairwise heuristic the algorithm then proceeds
+ through a number of refinement passes. Mustang reports the multiple
+ sequence alignment and the corresponding superposition of structures.
+ .
+ This package contains a larger set of test data than what
+ comes with the binary package.
Modified: trunk/packages/mustang/trunk/debian/copyright
===================================================================
--- trunk/packages/mustang/trunk/debian/copyright 2008-01-12 16:07:22 UTC (rev 1128)
+++ trunk/packages/mustang/trunk/debian/copyright 2008-01-13 22:20:17 UTC (rev 1129)
@@ -1,7 +1,8 @@
This package was downloaded from http://www.cs.mu.oz.au/~arun/mustang/
-Files: Makefile, src/*
-Copyright: (C) 2005, Arun S Konagurthu, The University of Melbourne.
+Files: Makefile, src/*, data/test/test_zf-CCHH
+Copyright: (C) 2005, Arun S Konagurthu <arun at bx.psu.edu> and The University
+ of Melbourne.
License: BSD-like
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
@@ -34,17 +35,44 @@
condition to the above license.
License: BDS-like
-XComment: Repackaging of the original tarball
- The upstream tarball was repackaged to remove PDB files which have an
- undetermined copyright status and hence cannot be distributed. Furthermore,
- the text of the license was added in the top level directory in the file
- `LICENSE'.
+Files: data/test/pdbs:
+Copyright: PD
+License:
+ ADVISORY NOTICE FOR USE OF THE PDB ARCHIVE
.
- The repackaging can be reproduced by running the following script:
+ By using the materials available in this archive, the user agrees to abide
+ by the following conditions:
.
- wget http://www.cs.mu.oz.au/~arun/mustang/mustang_v.3.tgz
- tar -xf mustang_v.3.tgz
- mv MUSTANG_v.3/ mustang-3.0.orig
- rm -rf mustang-3.0.orig/data/test/pdbs
- head -21 mustang-3.0.orig/src/main.cpp |tail -20 > mustang-3.0.orig/LICENSE
- GZIP=-9 tar -czf mustang_3.0.dfsg.orig.tar.gz mustang-3.0.orig
+ * The archival data files in the PDB archive are made freely available
+ to all users. Data files within the archive may be redistributed in original
+ form without restriction. Redistribution of modified data files using the same
+ file name as is on the FTP server is prohibited. The rules for file names are
+ detailed at http://www.wwpdb.org/wwpdb_charter.html.
+ .
+ * Data files containing PDB content may incorporate the PDB 4-letter entry
+ name (e.g. 1ABC) in standard PDB records only if they are exactly the same
+ as what is residing in the PDB archive. This does not prevent databases
+ from including PDB entry_id's as cross-references where it is clear that
+ they refer to the PDB archive. PDB records refer to the standard PDB format.
+ The distribution of modified PDB format data including the records: HEADER,
+ CAVEAT, REVDAT, SPRSDE, DBREF, SEQADV, and MODRES are not allowed.
+ .
+ * The user assumes all responsibility for insuring that intellectual property
+ claims associated with any data set deposited in the PDB archive are honored.
+ It should be understood that the PDB data files do not contain any information
+ on intellectual property claims with the exception in some cases of a reference
+ for a patent involving the structure.
+ .
+ * Any opinion, findings, and conclusions expressed in the PDB archive by the
+ authors/contributors do not necessarily reflect the views of the wwPDB.
+ .
+ * The data in the PDB archive are provided on an "as is" basis. The wwPDB
+ nor its comprising institutions cannot be held liable to any party for direct,
+ indirect, special, incidental, or consequential damages, including lost
+ profits, arising from the use of PDB materials.
+ .
+ * Resources on this site are provided without warranty of any kind, either
+ expressed or implied. This includes but is not limited to merchantability or
+ fitness for a particular purpose. The institutions managing this site make
+ no representation that these resources will not infringe any patent or other
+ proprietary right.
Modified: trunk/packages/mustang/trunk/debian/patches/test_zf-cchh.dpatch
===================================================================
--- trunk/packages/mustang/trunk/debian/patches/test_zf-cchh.dpatch 2008-01-12 16:07:22 UTC (rev 1128)
+++ trunk/packages/mustang/trunk/debian/patches/test_zf-cchh.dpatch 2008-01-13 22:20:17 UTC (rev 1129)
@@ -1,50 +1,18 @@
#! /bin/sh /usr/share/dpatch/dpatch-run
-## test_zf_cchh by Morten Kjeldgaard <mok at bioxray.dk>
+## test_zf_cchh by Morten Kjeldgaard <mok at bioxray.au.dk>
##
## DP: Fix the test command file so it makes use of the pdb entries
-## DP: that have been downloaded.
+## DP: in the right directory
@DPATCH@
+
diff -urNad mustang-3.0.orig~/data/test/test_zf-CCHH mustang-3.0.orig/data/test/test_zf-CCHH
--- mustang-3.0.orig~/data/test/test_zf-CCHH 2007-08-18 02:39:49.000000000 +0200
+++ mustang-3.0.orig/data/test/test_zf-CCHH 2007-08-18 02:40:05.000000000 +0200
-@@ -17,26 +17,26 @@
+@@ -17,7 +17,7 @@
###############################################################################################
- > ./data/test/pdbs
-+ > /tmp
-
--+1ard.pdb
--+1bboN.pdb
-- + 1paa.pdb
-+#+1ard.pdb
-+#+1bboN.pdb
-+# + 1paa.pdb
- +1sp1.pdb
- +1sp2.pdb
-
-- + 1zaa1.pdb
--+1zaa2.pdb
--+1zaa3.pdb
--+1zfd.pdb
-+# + 1zaa1.pdb
-+#+1zaa2.pdb
-+#+1zaa3.pdb
-+#+1zfd.pdb
-
-
--+1znf.pdb
--+1znm.pdb
--+2drp1.pdb
--+2drp2.pdb
-+#+1znf.pdb
-+#+1znm.pdb
-+#+2drp1.pdb
-+#+2drp2.pdb
- +3znf.pdb
-
--+5znf.pdb
-+#+5znf.pdb
- #+test1.pdb
- #+test2.pdb
++ > /usr/share/doc/mustang/examples/pdbs
+
Modified: trunk/packages/mustang/trunk/debian/rules
===================================================================
--- trunk/packages/mustang/trunk/debian/rules 2008-01-12 16:07:22 UTC (rev 1128)
+++ trunk/packages/mustang/trunk/debian/rules 2008-01-13 22:20:17 UTC (rev 1129)
@@ -4,68 +4,71 @@
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
+# This has to be exported to make some magic below work.
+export DH_OPTIONS
+
include /usr/share/dpatch/dpatch.make
-CPPFLAGS = -Wall -g
+CFLAGS = -Wall -g
ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
- CPPFLAGS += -O0
+ CFLAGS += -O0
else
- CPPFLAGS += -O2
+ CFLAGS += -O2
endif
get-orig-source:
- cd .. ; wget http://www.cs.mu.oz.au/~arun/mustang/mustang_v.3.tgz
- cd .. ; tar -xf mustang_v.3.tgz
- mv ../MUSTANG_v.3/ ../mustang-3.0.orig
- rm -rf ../mustang-3.0.orig/data/test/pdbs
- head -21 ../mustang-3.0.orig/src/main.cpp |tail -20 > ../mustang-3.0.orig/LICENSE
- GZIP=-9 tar -czf ../mustang_3.0.dfsg.orig.tar.gz ../mustang-3.0.orig
- rm -rf ../mustang-3.0.orig
+ wget http://www.cs.mu.oz.au/~arun/mustang/mustang_v.3.tgz -O ../mustang_3.0.orig.tar.gz
-build: build-stamp
+build: build-arch build-indep
-build-stamp: patch-stamp
+build-arch: build-arch-stamp
+build-arch-stamp:
dh_testdir
# Compile Mustang:
$(MAKE) CPPFLAGS="$(CPPFLAGS)"
+
touch $@
-clean: unpatch
+build-indep: build-indep-stamp
+ # get rid of the test?.pdf files, they are not used
+ # in the example
+ rm -f test/data/pdbs/test*.pdb
+
+build-indep-stamp:
+
+clean:
dh_testdir
dh_testroot
- rm -f build-stamp
+ rm -f build-arch-stamp build-indep-stamp
# Clean up after the build process.
rm -f obj/*.o
rm -f bin/MUSTANG_v.3
- dh_clean
+ dh_clean
-install: build
+install: install-indep install-arch
+install-indep:
dh_testdir
dh_testroot
- dh_clean -k
- dh_installdirs
+ dh_installexamples -i data/test/pdbs data/test/test_zf-CCHH
- #$(MAKE) DESTDIR=$(CURDIR)/debian/mustang install
+install-arch:
+ dh_testdir
+ dh_testroot
+ dh_installexamples -s debian/runtest debian/test_zf-CCHH-small
install -D -m755 bin/MUSTANG_v.3 debian/mustang/usr/bin/mustang
-binary-indep:
- # nothing to do here
-
-# Build architecture-dependent files here.
-binary-arch: build install
+binary-common:
dh_testdir
dh_testroot
- dh_installchangelogs
+ dh_installchangelogs
dh_installdocs
- dh_installexamples data/test/* debian/runtest
dh_installman
- dh_link
dh_strip
- dh_compress
+ dh_compress -X.pdb
dh_fixperms
dh_installdeb
dh_shlibdeps
@@ -73,7 +76,15 @@
dh_md5sums
dh_builddeb
-binary: binary-arch
-.PHONY: build clean binary-arch binary install
+# Build architecture independant packages using the common target.
+binary-indep: build-indep install-indep
+ $(MAKE) -f debian/rules DH_OPTIONS=-i binary-common
+# Build architecture dependant packages using the common target.
+binary-arch: build-arch install-arch
+ $(MAKE) -f debian/rules DH_OPTIONS=-s binary-common
+
+binary: binary-arch binary-indep
+.PHONY: build clean binary-indep binary-arch binary install install-indep install-arch
+
####
Modified: trunk/packages/mustang/trunk/debian/runtest
===================================================================
--- trunk/packages/mustang/trunk/debian/runtest 2008-01-12 16:07:22 UTC (rev 1128)
+++ trunk/packages/mustang/trunk/debian/runtest 2008-01-13 22:20:17 UTC (rev 1129)
@@ -14,7 +14,7 @@
}
# The process will run in this directory:
-tmdir=/tmp/mustang
+tmpdir=/tmp/mustang
savedir=$PWD
mkdir $tmpdir
@@ -22,7 +22,7 @@
pdb_fetch $entries
for f in $entries; do gzip -dc $f.pdb.gz > $f.pdb ; done
-mustang -f /usr/share/doc/mustang/examples/test_zf-CCHH
+mustang -f /usr/share/doc/mustang/examples/test_zf-CCHH-small
cd $savedir
echo Results are in $tmpdir/results.html and $tmpdir/results.pdb
Added: trunk/packages/mustang/trunk/debian/test_zf-CCHH-small
===================================================================
--- trunk/packages/mustang/trunk/debian/test_zf-CCHH-small (rev 0)
+++ trunk/packages/mustang/trunk/debian/test_zf-CCHH-small 2008-01-13 22:20:17 UTC (rev 1129)
@@ -0,0 +1,22 @@
+###############################################################################################
+## This is a valid desciption file. ##
+## ##
+## Line starting with '>' symbol is treated as PATH to the directory containing structures ##
+## to be aligned. ##
+## ##
+## Lines starting with '+' symbol are treated as file names. If PATH is specified (as in ##
+## this case), then only the filenames should be provided. However, if PATH line is NOT ##
+## provided, then the absolute/relative paths of the structure files should be provided. ##
+## ##
+## All the lines NOT starting with '>' and '+' are simply ignored. ##
+## ##
+## Do NOT use comments in the same lines containg PATH and FILENAMES. ##
+## ##
+## Whitespaces are intentionally inserted before and/or after '>' and --in some cases-- '+' ##
+## symbols to show that the whitespaces are ignored ##
+###############################################################################################
+
+ > /tmp
+
++1sp1.pdb
++1sp2.pdb
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