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@mrs> Wed, 18 Apr 2012 11:09:02 +0200 + -- Laszlo Kajan <[email protected]> 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 <[email protected]> +Uploaders: Maarten L. Hekkelman <[email protected]>, + Laszlo Kajan <[email protected]>, + Andreas Tille <[email protected]> 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 <[email protected]> Source: http://www.cmbi.ru.nl/dssp/ +Files: debian/* +Copyright: © 2012, Maarten L. Hekkelman <[email protected]> +License: Boost-1.0 + Files: * Copyright: © 2009-2012, Maarten L. Hekkelman <[email protected]> License: Boost-1.0 -Files: debian/* -Copyright: © 2012, Maarten L. Hekkelman <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
