FinkPorts

apbs stable port information

Package: apbs
Version: 1.3.0
Revision: 2
UseMaxBuildJobs: false
Source: http://downloads.sourceforge.net/project/%n/%n/%n-%v/%n-1.3-source.tar.gz
Source-MD5: f99a505365f07f6853979cfe2ef23365
Depends: readline5-shlibs, gcc46-shlibs, python27
BuildDepends: gcc46, python27, fink (>= 0.24.12)
BuildConflicts: g77, g95, fort77
Conflicts: maloc, maloc-mpi-lammpi, maloc-mpi-openmpi
Replaces: maloc, maloc-mpi-lammpi, maloc-mpi-openmpi
ConfigureParams: --disable-openmp --build=%m-apple-darwin`uname -r|cut -f1 -d.` --host=%m-apple-darwin`uname -r|cut -f1 -d.`
SetCFLAGS: -O3
Description: Adaptive Poisson-Boltzmann Solver
PatchFile: %n.patch
PatchFile-MD5: 2662144e3e3508a944902c0a5e29eaf1
PatchScript: <<
sed 's|@INSTALL_DIR@|%d|g' < %{PatchFile} | patch -p1
<<
CompileScript: <<
#!/bin/bash -efv
PATH=%p/bin:%p/sbin:${PATH} ; export PATH
source %p/bin/init.sh
perl -pi -e 's|PY_SHARED="-shared"|PY_SHARED="-bundle"|g' configure
BLAS_DIR='/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A'
py_path=%p/bin/python2.7 F77=gfortran ./configure %c --enable-python --with-python=%p/bin/python2.7 \
--disable-openmp --with-blas="-L${BLAS_DIR} -lblas -Wl,-framework -Wl,vecLib -Wl,-undefined -Wl,dynamic_lookup" FFLAGS="-O3"
perl -pi -e 's|\${prefix}/share|%i/share/%n|g' Makefile
perl -pi -e 's|\$\(DESTDIR\)\$\(libdir\)|share/apbs/lib|g' contrib/blas/Makefile
make
<<
InstallScript: <<
#!/bin/zsh -efv
rm -Rf **/CVS # fink validate complains if this junk is left behind.
perl -pi -e 's|/usr/bin/env python|%p/bin/python|g' examples/**/*.py
perl -pi -e 's|/usr/bin/env python|%p/bin/python|g' tools/**/*.py
rm -f **/*.o
#
# make install DESTDIR=%d
# install it ourselves:
mkdir -p %i/bin
/bin/cp bin/apbs bin/ApbsClient.py %i/bin/.
echo '#!%p/bin/python2.7' >| %i/bin/wsdl2py
echo "from ZSI.generate.commands import wsdl2py" >> %i/bin/wsdl2py
echo "wsdl2py()" >> %i/bin/wsdl2py
chmod a+x %i/bin/wsdl2py
#
mkdir -p %i/share/%n
/bin/cp -r examples %i/share/%n/.
/bin/cp -r tools %i/share/%n/.
/bin/cp -r doc %i/share/%n/.
#
mkdir -p %i/share/doc
ln -s %p/share/%n/doc %i/share/doc/%n
#
mkdir -p %i/lib/python2.7/site-packages/ZSI
/bin/cp -r contrib/opal/ZSI/ZSI/* %i/lib/python2.7/site-packages/ZSI/.
#
mkdir -p %i/include/apbs
/bin/cp **/*.h %i/include/apbs/.
#
mkdir -p %i/lib
/bin/rm -rf contrib
/bin/cp **/.*/*.a %i/lib/.
/bin/cp **/*.la %i/lib/.
ranlib %i/lib/*.a
#
<<
PreRmScript: <<
/usr/bin/find %p/lib/python2.7/site-packages/ZSI -name '*.pyo' -delete
<<
PostInstScript: <<
%p/bin/python2.7 -O %p/lib/python2.7/compileall.py -q %p/lib/python2.7/site-packages/ZSI
<<
################################################################################
SplitOff: <<
Package: %N-dev
BuildDependsOnly: true
Description: apbs headers, static libraries and libtool files
Files:<<
include/apbs
lib/*.a
lib/*.la
<<
<<
################################################################################
Homepage: http://apbs.sourceforge.net/
RunTimeVars: <<
APBS_PSIZE:%p/share/%n/tools/manip
<<
DescDetail: <<
APBS is a software package for the numerical solution of the
Poisson-Boltzmann equation, a popular continuum model for describing
electrostatic interactions between molecular solutes over a wide range
of length scales. The Fink pymol package is pre-configured to permit
apbs to be used as a plug-in.
.
The software is released under the GPL, but the author requests that you
register your use with him to aid him in obtaining funding to continue to
develop the code. Most electrostatics software is payware, so please help
him continue to support this free software. You can do so at this URL:
http://agave.wustl.edu/apbs/download/
<<
License: GPL
Maintainer: W. G. Scott

apbs stable port .patch

diff -ruN apbs-1.3-source/configure apbs-1.3-source-orig/configure
--- apbs-1.3-source/configure 2010-10-21 08:17:07.000000000 -0700
+++ apbs-1.3-source-orig/configure 2010-11-23 20:07:40.000000000 -0800
@@ -22371,7 +22371,7 @@

SERVICEURL='http://kryptonite.nbcr.net/opal2/services/apbs_1.3'
PARALLELSERVICEURL='http://oolite.calit2.optiputer.net/opal2/services/apbs-parallel-1.3'
-SITEPKGS=${prefix}/lib/python${PY_VERSION}/site-packages
+SITEPKGS=@INSTALL_DIR@${prefix}/lib/python${PY_VERSION}/site-packages


# Check whether --with-maxmem was given.
diff -ruN apbs-1.3-source/contrib/opal/ZSI/Makefile.in apbs-1.3-source-orig/contrib/opal/ZSI/Makefile.in
--- apbs-1.3-source/contrib/opal/ZSI/Makefile.in 2010-05-19 10:24:24.000000000 -0700
+++ apbs-1.3-source-orig/contrib/opal/ZSI/Makefile.in 2010-11-23 20:09:12.000000000 -0800
@@ -542,7 +542,7 @@

install-data-local:
-mkdir -p ${SITEPKGS}
- ${py_path} setup.py install --prefix=${prefix}
+ ${py_path} setup.py install --prefix=@INSTALL_DIR@${prefix}
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
.NOEXPORT:
diff -ruN apbs-1.3-source/tools/python/Makefile.in apbs-1.3-source-orig/tools/python/Makefile.in
--- apbs-1.3-source/tools/python/Makefile.in 2010-05-19 10:24:24.000000000 -0700
+++ apbs-1.3-source-orig/tools/python/Makefile.in 2010-11-23 20:11:08.000000000 -0800
@@ -52,7 +52,6 @@
${top_builddir}/bin/.libs/libapbsmainroutines.a \
${top_builddir}/src/aaa_lib/.libs/libapbs.a \
${top_builddir}/contrib/lib/libmaloc.a \
- ${top_builddir}/contrib/blas/.libs/libapbsblas.a \
$(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
DEFAULT_INCLUDES = -I. -I$(top_builddir)/src/aaa_inc@am__isrc@
depcomp =
@@ -248,7 +247,7 @@
SUBDIRS = vgrid
_apbslib_so_SOURCES = apbslib.c
_apbslib_so_LINK = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
-_apbslib_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a ${top_builddir}/contrib/lib/libmaloc.a ${top_builddir}/contrib/blas/.libs/libapbsblas.a $(PY_LDFLAGS) ${z_lib}
+_apbslib_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a ${top_builddir}/contrib/lib/libmaloc.a $(PY_LDFLAGS) ${z_lib}
all: all-recursive

.SUFFIXES:

apbs _unstable_ port information

Package: apbs
Version: 1.3.0
Revision: 2
Source: http://downloads.sourceforge.net/project/%n/%n/%n-%v/%n-1.3-source.tar.gz
Source-MD5: f99a505365f07f6853979cfe2ef23365
Depends: readline5-shlibs, gnuplot (>=4.2.0) | gnuplot-nox | gnuplot-nogtk, pdb2pqr, gcc44-shlibs, python27
BuildDepends: gcc44, python27, fink (>= 0.24.12)
BuildConflicts: g77, g95, fort77
Conflicts: maloc, maloc-mpi-lammpi, maloc-mpi-openmpi
Replaces: maloc, maloc-mpi-lammpi, maloc-mpi-openmpi
ConfigureParams: --disable-openmp --build=%m-apple-darwin`uname -r|cut -f1 -d.` --host=%m-apple-darwin`uname -r|cut -f1 -d.`
SetCFLAGS: -O3
Description: Adaptive Poisson-Boltzmann Solver
PatchFile: %n.patch
PatchFile-MD5: 2662144e3e3508a944902c0a5e29eaf1
PatchScript: <<
sed 's|@INSTALL_DIR@|%d|g' < %{PatchFile} | patch -p1
<<
UseMaxBuildJobs: false
CompileScript: <<
#!/bin/bash -efv
PATH=%p/bin:%p/sbin:${PATH} ; export PATH
source %p/bin/init.sh
BLAS_DIR='/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A'
py_path=%p/bin/python2.7 F77=gfortran ./configure %c --enable-python --with-python=%p/bin/python2.7 \
--disable-openmp --with-blas="-L${BLAS_DIR} -lblas -Wl,-framework -Wl,vecLib -Wl,-undefined -Wl,dynamic_lookup" FFLAGS="-O3"
perl -pi -e 's|\${prefix}/share|%i/share/%n|g' Makefile
perl -pi -e 's|\$\(DESTDIR\)\$\(libdir\)|share/apbs/lib|g' contrib/blas/Makefile
make
<<
InstallScript: <<
#!/bin/zsh -efv
rm -Rf **/CVS # fink validate complains if this junk is left behind.
perl -pi -e 's|/usr/bin/env python|%p/bin/python|g' examples/**/*.py
perl -pi -e 's|/usr/bin/env python|%p/bin/python|g' tools/**/*.py
rm -f **/*.o
#
# make install DESTDIR=%d
# install it ourselves:
mkdir -p %i/bin
/bin/cp bin/apbs bin/ApbsClient.py %i/bin/.
echo '#!%p/bin/python2.7' >| %i/bin/wsdl2py
echo "from ZSI.generate.commands import wsdl2py" >> %i/bin/wsdl2py
echo "wsdl2py()" >> %i/bin/wsdl2py
chmod a+x %i/bin/wsdl2py
#
mkdir -p %i/share/%n
/bin/cp -r examples %i/share/%n/.
/bin/cp -r tools %i/share/%n/.
/bin/cp -r doc %i/share/%n/.
#
mkdir -p %i/share/doc
ln -s %p/share/%n/doc %i/share/doc/%n
#
mkdir -p %i/lib/python2.7/site-packages/ZSI
/bin/cp -r contrib/opal/ZSI/ZSI/* %i/lib/python2.7/site-packages/ZSI/.
#
mkdir -p %i/include/apbs
/bin/cp **/*.h %i/include/apbs/.
#
mkdir -p %i/lib
/bin/rm -rf contrib
/bin/cp **/.*/*.a %i/lib/.
/bin/cp **/*.la %i/lib/.
ranlib %i/lib/*.a
#
<<
PreRmScript: <<
/usr/bin/find %p/lib/python2.7/site-packages/ZSI -name '*.pyo' -delete
<<
PostInstScript: <<
%p/bin/python2.7 -O %p/lib/python2.7/compileall.py -q %p/lib/python2.7/site-packages/ZSI
# per request of software's author
echo ""
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "Please issue \"open http://agave.wustl.edu/apbs/download/\","
echo "to register your use of this software to help the author"
echo "maintain funding for apbs. apbs is released under the GPL and this is"
echo "not required, but would be very helpful."
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo ""
sleep 5
<<
################################################################################
SplitOff: <<
Package: %N-dev
BuildDependsOnly: true
Description: apbs headers, static libraries and libtool files
Files:<<
include/apbs
lib/*.a
lib/*.la
<<
<<
################################################################################
Homepage: http://apbs.sourceforge.net/
RunTimeVars: <<
APBS_PSIZE:%p/share/%n/tools/manip
<<
DescDetail: <<
APBS is a software package for the numerical solution of the
Poisson-Boltzmann equation, a popular continuum model for describing
electrostatic interactions between molecular solutes over a wide range
of length scales. The Fink pymol package is pre-configured to permit
apbs to be used as a plug-in.
.
The software is released under the GPL, but the author requests that you
register your use with him to aid him in obtaining funding to continue to
develop the code. Most electrostatics software is payware, so please help
him continue to support this free software. You can do so at this URL:
http://agave.wustl.edu/apbs/download/
<<
License: GPL
Maintainer: W. G. Scott

apbs _unstable_ port .patch

diff -ruN apbs-1.3-source/configure apbs-1.3-source-orig/configure
--- apbs-1.3-source/configure 2010-10-21 08:17:07.000000000 -0700
+++ apbs-1.3-source-orig/configure 2010-11-23 20:07:40.000000000 -0800
@@ -22371,7 +22371,7 @@

SERVICEURL='http://kryptonite.nbcr.net/opal2/services/apbs_1.3'
PARALLELSERVICEURL='http://oolite.calit2.optiputer.net/opal2/services/apbs-parallel-1.3'
-SITEPKGS=${prefix}/lib/python${PY_VERSION}/site-packages
+SITEPKGS=@INSTALL_DIR@${prefix}/lib/python${PY_VERSION}/site-packages


# Check whether --with-maxmem was given.
diff -ruN apbs-1.3-source/contrib/opal/ZSI/Makefile.in apbs-1.3-source-orig/contrib/opal/ZSI/Makefile.in
--- apbs-1.3-source/contrib/opal/ZSI/Makefile.in 2010-05-19 10:24:24.000000000 -0700
+++ apbs-1.3-source-orig/contrib/opal/ZSI/Makefile.in 2010-11-23 20:09:12.000000000 -0800
@@ -542,7 +542,7 @@

install-data-local:
-mkdir -p ${SITEPKGS}
- ${py_path} setup.py install --prefix=${prefix}
+ ${py_path} setup.py install --prefix=@INSTALL_DIR@${prefix}
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
.NOEXPORT:
diff -ruN apbs-1.3-source/tools/python/Makefile.in apbs-1.3-source-orig/tools/python/Makefile.in
--- apbs-1.3-source/tools/python/Makefile.in 2010-05-19 10:24:24.000000000 -0700
+++ apbs-1.3-source-orig/tools/python/Makefile.in 2010-11-23 20:11:08.000000000 -0800
@@ -52,7 +52,6 @@
${top_builddir}/bin/.libs/libapbsmainroutines.a \
${top_builddir}/src/aaa_lib/.libs/libapbs.a \
${top_builddir}/contrib/lib/libmaloc.a \
- ${top_builddir}/contrib/blas/.libs/libapbsblas.a \
$(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
DEFAULT_INCLUDES = -I. -I$(top_builddir)/src/aaa_inc@am__isrc@
depcomp =
@@ -248,7 +247,7 @@
SUBDIRS = vgrid
_apbslib_so_SOURCES = apbslib.c
_apbslib_so_LINK = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
-_apbslib_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a ${top_builddir}/contrib/lib/libmaloc.a ${top_builddir}/contrib/blas/.libs/libapbsblas.a $(PY_LDFLAGS) ${z_lib}
+_apbslib_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a ${top_builddir}/contrib/lib/libmaloc.a $(PY_LDFLAGS) ${z_lib}
all: all-recursive

.SUFFIXES:

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