Author: manuel Date: 2011-08-30 22:29:31 +0000 (Tue, 30 Aug 2011) New Revision: 7599
Added: trunk/packages/pdb2pqr/tags/1.7-2/ trunk/packages/pdb2pqr/tags/1.7-2/debian/changelog trunk/packages/pdb2pqr/tags/1.7-2/debian/control trunk/packages/pdb2pqr/tags/1.7-2/debian/rules Removed: trunk/packages/pdb2pqr/tags/1.7-2/debian/changelog trunk/packages/pdb2pqr/tags/1.7-2/debian/control trunk/packages/pdb2pqr/tags/1.7-2/debian/rules Log: [svn-buildpackage] Tagging pdb2pqr 1.7-2 Deleted: trunk/packages/pdb2pqr/tags/1.7-2/debian/changelog =================================================================== --- trunk/packages/pdb2pqr/trunk/debian/changelog 2011-08-26 13:24:12 UTC (rev 7556) +++ trunk/packages/pdb2pqr/tags/1.7-2/debian/changelog 2011-08-30 22:29:31 UTC (rev 7599) @@ -1,5 +0,0 @@ -pdb2pqr (1.7-1) unstable; urgency=low - - * New upstream release. Closes: #416269, #420734. - - -- Manuel Prinz <[email protected]> Sun, 30 Jan 2011 11:53:54 +0100 Copied: trunk/packages/pdb2pqr/tags/1.7-2/debian/changelog (from rev 7598, trunk/packages/pdb2pqr/trunk/debian/changelog) =================================================================== --- trunk/packages/pdb2pqr/tags/1.7-2/debian/changelog (rev 0) +++ trunk/packages/pdb2pqr/tags/1.7-2/debian/changelog 2011-08-30 22:29:31 UTC (rev 7599) @@ -0,0 +1,12 @@ +pdb2pqr (1.7-2) unstable; urgency=low + + * Pass -fPIC to compiler on all architectures. Closes: 636204. LP: 791313. + * Bumped Standards-Version to 3.9.2. No changes needed. + + -- Manuel Prinz <[email protected]> Wed, 31 Aug 2011 00:22:15 +0200 + +pdb2pqr (1.7-1) unstable; urgency=low + + * New upstream release. Closes: #416269, #420734. + + -- Manuel Prinz <[email protected]> Sun, 30 Jan 2011 11:53:54 +0100 Deleted: trunk/packages/pdb2pqr/tags/1.7-2/debian/control =================================================================== --- trunk/packages/pdb2pqr/trunk/debian/control 2011-08-26 13:24:12 UTC (rev 7556) +++ trunk/packages/pdb2pqr/tags/1.7-2/debian/control 2011-08-30 22:29:31 UTC (rev 7599) @@ -1,56 +0,0 @@ -Source: pdb2pqr -Section: science -Priority: optional -Maintainer: DebiChem Team <[email protected]> -DM-Upload-Allowed: yes -Uploaders: Steffen Moeller <[email protected]>, Manuel Prinz <[email protected]>, - Andreas Tille <[email protected]> -Build-Depends: debhelper (>= 7.0.50~), gfortran, swig, xmlto, openbabel, - python-support, python-dev, python-numpy, - autoconf, automake, libtool, autotools-dev -Standards-Version: 3.9.1 -XS-Python-Version: 2.6 -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/pdb2pqr/trunk/?rev=0&sc=0 -Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/pdb2pqr/trunk/ -Homepage: http://pdb2pqr.poissonboltzmann.org/pdb2pqr/ - -Package: pdb2pqr -XB-Python-Version: ${python:Versions} -Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, python-numpy -Suggests: apbs -Enhances: autodocktools -Description: Preparation of protein structures for electrostatics calculations - PDB2PQR is a Python software package that automates many of the common - tasks of preparing structures for continuum electrostatics calculations. - It thus provides a platform-independent utility for converting protein files - in PDB format to PQR format. These tasks include: - * Adding a limited number of missing heavy atoms to biomolecular structures - * Determining side-chain pKas - * Placing missing hydrogens - * Optimizing the protein for favorable hydrogen bonding - * Assigning charge and radius parameters from a variety of force fields - -Package: pdb2pqr-doc -Section: doc -Architecture: all -Depends: ${misc:Depends} -Recommends: pdb2pqr -Description: example files accompanying pdb2pqr - Files containing protein structures tend to become large very quickly and - most users of this package will refrain from their installation, particularly - on larger clusters. - -Package: propka -Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends} -Suggests: pdb2pqr -Description: Modify the protonation state of protein structures - PropKa is a tool to modify the protonation state of a protein structure - in the Protein Data Bank (PDB) format to match a given pKa value. - It can also be used to refine NMR structures, which often yield - inaccurate pKa values for some residues. - . - The PROPKA method is described in Hui Li, Andrew D. Robertson, and - Jan H. Jensen "Very Fast Empirical Prediction and Interpretation of - Protein pKa Values" Proteins, 2005, 61, 704-721 Copied: trunk/packages/pdb2pqr/tags/1.7-2/debian/control (from rev 7597, trunk/packages/pdb2pqr/trunk/debian/control) =================================================================== --- trunk/packages/pdb2pqr/tags/1.7-2/debian/control (rev 0) +++ trunk/packages/pdb2pqr/tags/1.7-2/debian/control 2011-08-30 22:29:31 UTC (rev 7599) @@ -0,0 +1,56 @@ +Source: pdb2pqr +Section: science +Priority: optional +Maintainer: DebiChem Team <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Steffen Moeller <[email protected]>, Manuel Prinz <[email protected]>, + Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 7.0.50~), gfortran, swig, xmlto, openbabel, + python-support, python-dev, python-numpy, + autoconf, automake, libtool, autotools-dev +Standards-Version: 3.9.2 +XS-Python-Version: 2.6 +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/pdb2pqr/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/pdb2pqr/trunk/ +Homepage: http://pdb2pqr.poissonboltzmann.org/pdb2pqr/ + +Package: pdb2pqr +XB-Python-Version: ${python:Versions} +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, python-numpy +Suggests: apbs +Enhances: autodocktools +Description: Preparation of protein structures for electrostatics calculations + PDB2PQR is a Python software package that automates many of the common + tasks of preparing structures for continuum electrostatics calculations. + It thus provides a platform-independent utility for converting protein files + in PDB format to PQR format. These tasks include: + * Adding a limited number of missing heavy atoms to biomolecular structures + * Determining side-chain pKas + * Placing missing hydrogens + * Optimizing the protein for favorable hydrogen bonding + * Assigning charge and radius parameters from a variety of force fields + +Package: pdb2pqr-doc +Section: doc +Architecture: all +Depends: ${misc:Depends} +Recommends: pdb2pqr +Description: example files accompanying pdb2pqr + Files containing protein structures tend to become large very quickly and + most users of this package will refrain from their installation, particularly + on larger clusters. + +Package: propka +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Suggests: pdb2pqr +Description: Modify the protonation state of protein structures + PropKa is a tool to modify the protonation state of a protein structure + in the Protein Data Bank (PDB) format to match a given pKa value. + It can also be used to refine NMR structures, which often yield + inaccurate pKa values for some residues. + . + The PROPKA method is described in Hui Li, Andrew D. Robertson, and + Jan H. Jensen "Very Fast Empirical Prediction and Interpretation of + Protein pKa Values" Proteins, 2005, 61, 704-721 Deleted: trunk/packages/pdb2pqr/tags/1.7-2/debian/rules =================================================================== --- trunk/packages/pdb2pqr/trunk/debian/rules 2011-08-26 13:24:12 UTC (rev 7556) +++ trunk/packages/pdb2pqr/tags/1.7-2/debian/rules 2011-08-30 22:29:31 UTC (rev 7599) @@ -1,49 +0,0 @@ -#!/usr/bin/make -f -# -*- mode: makefile; coding: utf-8 -*- - -PACKAGE := $(firstword $(shell dh_listpackages)) -VERSION := $(shell dpkg-parsechangelog | awk '/^Version:/ { print $$2 }') -UPSTREAM := $(shell echo "$(VERSION)" | sed 's/-.\+$$//') - -%: - dh $@ - -# Disable tests, as they need an internet connection to download files -override_dh_auto_test: - -override_dh_auto_install: -# Fix !#/bin/env shebang: substitute with #!/usr/bin/python - sed -i -e '1c#!/usr/bin/python' pdb2pka/inputgen_pKa.py -# Install Debian-provided stuff -# Install wrappers - for app in /usr/share/pdb2pqr/pdb2pqr.py /usr/share/pdb2pqr/src/psize.py; do \ - sed -e "s,@SCRIPT@,$${app}," debian/wrapper.sh \ - >debian/pdb2pqr/usr/bin/$$(basename $${app} .py) && \ - chmod 0755 debian/pdb2pqr/usr/bin/$$(basename $${app} .py); \ - done -# Install man pages - xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/pdb2pqr.1.xml - xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/psize.1.xml - xmlto -o debian/propka/usr/share/man/man1/ man debian/propka.1.xml - dh_auto_install - -override_dh_fixperms: - dh_fixperms - chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/main.py - chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/main_cgi.py - chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/ligandclean/__init__.py - chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pka_routines.py - chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pKaIO_compat.py - chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pKa_utility_functions_compat.py - -.PHONY: get-orig-source -get-orig-source: - rm -rf get-orig-source - mkdir -p get-orig-source - uscan --no-conf --no-symlink --force-download --download-current-version --destdir=get-orig-source - tar xzf get-orig-source/$(PACKAGE)-$(UPSTREAM).tar.gz -C get-orig-source \ - --exclude="contrib" \ - --exclude="jmol" - mv get-orig-source/$(PACKAGE)-$(UPSTREAM) get-orig-source/$(PACKAGE)-$(UPSTREAM).repack - GZIP='--best --no-name' tar czf ../$(PACKAGE)_$(UPSTREAM).orig.tar.gz -C get-orig-source $(PACKAGE)-$(UPSTREAM).repack - rm -rf get-orig-source Copied: trunk/packages/pdb2pqr/tags/1.7-2/debian/rules (from rev 7596, trunk/packages/pdb2pqr/trunk/debian/rules) =================================================================== --- trunk/packages/pdb2pqr/tags/1.7-2/debian/rules (rev 0) +++ trunk/packages/pdb2pqr/tags/1.7-2/debian/rules 2011-08-30 22:29:31 UTC (rev 7599) @@ -0,0 +1,53 @@ +#!/usr/bin/make -f +# -*- mode: makefile; coding: utf-8 -*- + +PACKAGE := $(firstword $(shell dh_listpackages)) +VERSION := $(shell dpkg-parsechangelog | awk '/^Version:/ { print $$2 }') +UPSTREAM := $(shell echo "$(VERSION)" | sed 's/-.\+$$//') + +%: + dh $@ + +# Compile with -fPIC on all platforms (fix for #636204) +override_dh_auto_configure: + dh_auto_configure -- CFLAGS="$(dpkg-buildflags --get CFLAGS) -fPIC" FFLAGS="$(dpkg-buildflags --get FFLAGS) -fPIC" + +# Disable tests, as they need an internet connection to download files +override_dh_auto_test: + +override_dh_auto_install: +# Fix !#/bin/env shebang: substitute with #!/usr/bin/python + sed -i -e '1c#!/usr/bin/python' pdb2pka/inputgen_pKa.py +# Install Debian-provided stuff +# Install wrappers + for app in /usr/share/pdb2pqr/pdb2pqr.py /usr/share/pdb2pqr/src/psize.py; do \ + sed -e "s,@SCRIPT@,$${app}," debian/wrapper.sh \ + >debian/pdb2pqr/usr/bin/$$(basename $${app} .py) && \ + chmod 0755 debian/pdb2pqr/usr/bin/$$(basename $${app} .py); \ + done +# Install man pages + xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/pdb2pqr.1.xml + xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/psize.1.xml + xmlto -o debian/propka/usr/share/man/man1/ man debian/propka.1.xml + dh_auto_install + +override_dh_fixperms: + dh_fixperms + chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/main.py + chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/main_cgi.py + chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/ligandclean/__init__.py + chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pka_routines.py + chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pKaIO_compat.py + chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pKa_utility_functions_compat.py + +.PHONY: get-orig-source +get-orig-source: + rm -rf get-orig-source + mkdir -p get-orig-source + uscan --no-conf --no-symlink --force-download --download-current-version --destdir=get-orig-source + tar xzf get-orig-source/$(PACKAGE)-$(UPSTREAM).tar.gz -C get-orig-source \ + --exclude="contrib" \ + --exclude="jmol" + mv get-orig-source/$(PACKAGE)-$(UPSTREAM) get-orig-source/$(PACKAGE)-$(UPSTREAM).repack + GZIP='--best --no-name' tar czf ../$(PACKAGE)_$(UPSTREAM).orig.tar.gz -C get-orig-source $(PACKAGE)-$(UPSTREAM).repack + rm -rf get-orig-source _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
