[med-svn] r10403 - in trunk/packages/dssp/trunk/debian: . patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Wed Apr 18 14:57:16 UTC 2012
Author: lkajan-guest
Date: 2012-04-18 14:57:16 +0000 (Wed, 18 Apr 2012)
New Revision: 10403
Added:
trunk/packages/dssp/trunk/debian/dssp.install
trunk/packages/dssp/trunk/debian/upstream
Modified:
trunk/packages/dssp/trunk/debian/
trunk/packages/dssp/trunk/debian/changelog
trunk/packages/dssp/trunk/debian/control
trunk/packages/dssp/trunk/debian/copyright
trunk/packages/dssp/trunk/debian/patches/makefile
trunk/packages/dssp/trunk/debian/rules
trunk/packages/dssp/trunk/debian/watch
Log:
added description to dssp; added upstream (reference) to dssp; parallel building now enabled; fixed spelling error in man page; added debug package; fixed debian/watch; added get-orig-source target to rules;
Property changes on: trunk/packages/dssp/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Modified: trunk/packages/dssp/trunk/debian/changelog
===================================================================
--- trunk/packages/dssp/trunk/debian/changelog 2012-04-18 11:10:22 UTC (rev 10402)
+++ trunk/packages/dssp/trunk/debian/changelog 2012-04-18 14:57:16 UTC (rev 10403)
@@ -1,5 +1,5 @@
dssp (2.0.4-1) UNRELEASED; urgency=low
- * Initial release. (Closes: #XXXXXX)
+ * Initial release. (Closes: #669259)
- -- Maarten L. Hekkelman <maarten at mrs> Wed, 18 Apr 2012 11:09:02 +0200
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 18 Apr 2012 11:09:02 +0200
Modified: trunk/packages/dssp/trunk/debian/control
===================================================================
--- trunk/packages/dssp/trunk/debian/control 2012-04-18 11:10:22 UTC (rev 10402)
+++ trunk/packages/dssp/trunk/debian/control 2012-04-18 14:57:16 UTC (rev 10403)
@@ -1,19 +1,44 @@
Source: dssp
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Maarten L. Hekkelman <m.hekkelman at cmbi.ru.nl>,
+ Laszlo Kajan <lkajan at rostlab.org>,
+ Andreas Tille <tille at debian.org>
Build-Depends: debhelper (>= 7.0.50~),
- libboost1.46-dev (>= 1.46.1),
- libboost-filesystem1.46-dev (>= 1.46.1),
- libboost-iostreams1.46-dev (>= 1.46.1),
- libboost-program-options1.46-dev (>= 1.46.1),
- libboost-system1.46-dev (>= 1.46.1),
- libboost-thread1.46-dev (>= 1.46.1)
-Standards-Version: 3.9.1
+ libboost-filesystem-dev (>= 1.46.1),
+ libboost-iostreams-dev (>= 1.46.1),
+ libboost-program-options-dev (>= 1.46.1),
+ libboost-system-dev (>= 1.46.1),
+ libboost-thread-dev (>= 1.46.1)
+Standards-Version: 3.9.3
Section: science
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/dssp/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/dssp/trunk/
+DM-Upload-Allowed: yes
Homepage: http://www.cmbi.ru.nl/dssp.html
Package: dssp
Architecture: any
Depends: ${misc:Depends}, ${shlibs:Depends}
-Description: DSSP is an application you use to calculate the
- secondary structure of a protein.
+Description: protein secondary structure assignment based on 3D structure
+ DSSP is an application you use to assign the secondary structure of a protein
+ based on its solved three dimensional (3D) structure.
+ .
+ This version (2) of DSSP is a rewrite that produces the same output as the
+ original DSSP, but deals better with exceptions in PDB files and is much
+ faster.
+
+Package: dssp-dbg
+Architecture: any
+Section: debug
+Priority: extra
+Depends: dssp (= ${binary:Version}), ${misc:Depends}
+Description: debugging symbols for dssp
+ DSSP is an application to assign the secondary structure of a protein
+ based on its three dimensional (3D) structure.
+ .
+ This version (2) of DSSP is a rewrite that produces the same output as the
+ original DSSP, but deals better with exceptions in PDB files and is much
+ faster.
+ .
+ This package provides the detached debug symbols for dssp.
Modified: trunk/packages/dssp/trunk/debian/copyright
===================================================================
--- trunk/packages/dssp/trunk/debian/copyright 2012-04-18 11:10:22 UTC (rev 10402)
+++ trunk/packages/dssp/trunk/debian/copyright 2012-04-18 14:57:16 UTC (rev 10403)
@@ -1,17 +1,17 @@
-Format: http://dep.debian.net/deps/dep5/
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: dssp
Upstream-Contact: Maarten L. Hekkelman <m.hekkelman at cmbi.ru.nl>
Source: http://www.cmbi.ru.nl/dssp/
+Files: debian/*
+Copyright: © 2012, Maarten L. Hekkelman <m.hekkelman at cmbi.ru.nl>
+License: Boost-1.0
+
Files: *
Copyright: © 2009-2012, Maarten L. Hekkelman <m.hekkelman at cmbi.ru.nl>
License: Boost-1.0
-Files: debian/*
-Copyright: © 2012, Maarten L. Hekkelman <m.hekkelman at cmbi.ru.nl>
License: Boost-1.0
-
-License: Boost-1.0
Boost Software License - Version 1.0 - August 17th, 2003
.
Permission is hereby granted, free of charge, to any person or organization
@@ -35,3 +35,4 @@
FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.
+
Added: trunk/packages/dssp/trunk/debian/dssp.install
===================================================================
--- trunk/packages/dssp/trunk/debian/dssp.install (rev 0)
+++ trunk/packages/dssp/trunk/debian/dssp.install 2012-04-18 14:57:16 UTC (rev 10403)
@@ -0,0 +1 @@
+usr/
Modified: trunk/packages/dssp/trunk/debian/patches/makefile
===================================================================
--- trunk/packages/dssp/trunk/debian/patches/makefile 2012-04-18 11:10:22 UTC (rev 10402)
+++ trunk/packages/dssp/trunk/debian/patches/makefile 2012-04-18 14:57:16 UTC (rev 10403)
@@ -1,11 +1,14 @@
--- a/makefile
+++ b/makefile
-@@ -11,23 +11,19 @@
+@@ -9,25 +9,21 @@
+ # new one if it doesn't exist. In this make.config you can set site
+ # specific variables like the Boost library location.
- firstTarget: mkdssp
+-firstTarget: mkdssp
+-
+-include make.config
++all: mkdssp
--include make.config
--
VERSION = 2.0.4
-DEST_DIR ?= /usr/local/
@@ -21,7 +24,8 @@
+LIBS = $(BOOST_LIBS:%=boost_%)
DEFINES = USE_COMPRESSION LINUX VERSION='"$(VERSION)"'
- CC = c++
+-CC = c++
++CXX = g++
-CFLAGS = $(INC_DIR:%=-I%) -iquote src -g -Wall -Wno-multichar -pthread
-LDOPTS = $(LIB_DIR:%=-L%) $(LIBS:%=-l%) -g -pthread
@@ -30,17 +34,31 @@
OBJ_DIR = obj
-@@ -49,7 +45,8 @@
+@@ -48,25 +44,21 @@
+ OBJECTS = $(OBJ_DIR)/mkdssp.o $(OBJ_DIR)/dssp.o $(OBJ_DIR)/primitives-3d.o $(OBJ_DIR)/structure.o $(OBJ_DIR)/utils.o
mkdssp: $(OBJECTS)
- @ echo linking $@
+- @ echo linking $@
- @ $(CC) -static -o $@ $^ $(LDOPTS)
-+ @ $(CC) -o $@ $^ $(LDOPTS)
-+ @ strip $@
- @ echo OK
+- @ echo OK
+-
+-include $(OBJECTS:%.o=%.d)
+-
+-$(OBJECTS:.o=.d):
+-
+-$(OBJ_DIR)/%.o: %.cpp
+- @ if [ ! -d $(OBJ_DIR) ]; then mkdir $(OBJ_DIR); fi
+- @ echo compiling $@
+- @ $(CC) -MD -c -o $@ $< $(CFLAGS)
++ $(CXX) -o $@ $^ $(LDOPTS)
++
++$(OBJ_DIR):
++ mkdir -p $(OBJ_DIR)
++
++$(OBJ_DIR)/%.o: %.cpp | $(OBJ_DIR)
++ $(CXX) -MD -c -o $@ $< $(CFLAGS)
- include $(OBJECTS:%.o=%.d)
-@@ -65,8 +62,9 @@
+ clean:
rm -rf $(OBJ_DIR)/* mkdssp
install: mkdssp
@@ -52,7 +70,7 @@
dist: $(OBJECTS)
@ rm -rf $(DIST_NAME)
-@@ -81,11 +79,3 @@
+@@ -81,11 +73,3 @@
@ cp doc/mkdssp.1 $(DIST_NAME)/doc/mkdssp.1
tar czf $(DIST_NAME).tgz $(DIST_NAME)
cp $(DIST_NAME).tgz dssp_$(VERSION).orig.tar.gz
@@ -64,3 +82,14 @@
- @echo "#BOOST_LIB_DIR = $(HOME)/projects/boost/lib" >> make.config
- @echo "#BOOST_INC_DIR = $(HOME)/projects/boost/include" >> make.config
-
+--- a/doc/mkdssp.1
++++ b/doc/mkdssp.1
+@@ -159,7 +159,7 @@
+ .SH TODO
+ The code desperately needs an update. The first thing that needs
+ implementing is the improved recognition of pi\-helices. A second
+-improvement would be to use angle dependant H\-bond energy calculation.
++improvement would be to use angle dependent H\-bond energy calculation.
+ .SH BUGS
+ If you find any, please let me know.
+ .SH AUTHOR
Modified: trunk/packages/dssp/trunk/debian/rules
===================================================================
--- trunk/packages/dssp/trunk/debian/rules 2012-04-18 11:10:22 UTC (rev 10402)
+++ trunk/packages/dssp/trunk/debian/rules 2012-04-18 14:57:16 UTC (rev 10403)
@@ -1,4 +1,15 @@
#!/usr/bin/make -f
+DH_VERBOSE := 1
+
%:
- dh $@
+ dh $@ --parallel
+
+.PHONY: override_dh_strip
+override_dh_strip:
+ dh_strip --dbg-package=dssp-dbg
+
+.PHONY: get-orig-source
+get-orig-source:
+ mkdir -p ../tarballs
+ uscan --verbose --force-download --destdir=../tarballs
Added: trunk/packages/dssp/trunk/debian/upstream
===================================================================
--- trunk/packages/dssp/trunk/debian/upstream (rev 0)
+++ trunk/packages/dssp/trunk/debian/upstream 2012-04-18 14:57:16 UTC (rev 10403)
@@ -0,0 +1,10 @@
+Name: dssp
+Reference:
+ - Author: Kabsch W, Sander C
+ Title: 'Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.'
+ Journal: Biopolymers
+ Volume: 22
+ Pages: 2577-2637
+ Year: 1983
+ URL: http://www.ncbi.nlm.nih.gov/pubmed/6667333
+ PMID: 6667333
Modified: trunk/packages/dssp/trunk/debian/watch
===================================================================
--- trunk/packages/dssp/trunk/debian/watch 2012-04-18 11:10:22 UTC (rev 10402)
+++ trunk/packages/dssp/trunk/debian/watch 2012-04-18 14:57:16 UTC (rev 10403)
@@ -1,2 +1,3 @@
-version=2.0.4
-ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-([0-9.]+).tbz
+version=3
+opts="pasv" \
+ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-([0-9.]+)\.t[bgx]z debian uupdate
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