[135278] trunk/dports/science/pdb2pqr/Portfile
ryandesign at macports.org
ryandesign at macports.org
Tue Apr 21 16:39:46 PDT 2015
Revision: 135278
https://trac.macports.org/changeset/135278
Author: ryandesign at macports.org
Date: 2015-04-21 16:39:46 -0700 (Tue, 21 Apr 2015)
Log Message:
-----------
pdb2pqr: update to 2.0.0 (#47254; maintainer)
Modified Paths:
--------------
trunk/dports/science/pdb2pqr/Portfile
Modified: trunk/dports/science/pdb2pqr/Portfile
===================================================================
--- trunk/dports/science/pdb2pqr/Portfile 2015-04-21 22:49:42 UTC (rev 135277)
+++ trunk/dports/science/pdb2pqr/Portfile 2015-04-21 23:39:46 UTC (rev 135278)
@@ -5,8 +5,7 @@
PortGroup python 1.0
name pdb2pqr
-version 1.7
-revision 2
+version 2.0.0
categories science
maintainers gmail.com:howarth.at.macports
description automate Poisson-Boltzmann electrostatics calculations
@@ -16,85 +15,52 @@
protein files in PDB format to PQR format.
homepage http://pdb2pqr.sourceforge.net/
platforms darwin
-master_sites sourceforge
-checksums md5 058622cb2ca6ca12af04d4f11b272951 \
- sha1 df2bf4303dbc64b69a20d48331386d8c08c234f1
+master_sites sourceforge:project/pdb2pqr/pdb2pqr/pdb2pqr-${version}/
+distfiles ${name}-src-${version}.tar.gz
+checksums md5 e4d50d3057778f051f49cc385909b293 \
+ sha1 77285efe9b78c8bd2df61b977eed8cca71df7ace
-python.default_version 26
+python.default_version 27
-use_parallel_build no
-use_configure yes
-build.cmd make
-build.target all
+worksrcdir ${name}-src-${version}
+
depends_lib port:py${python.version}-numeric
post-patch {
- reinplace "s|fort xlf95 lf95 g95|${configure.f77}|g" ${worksrcpath}/propka/configure
- reinplace "s|/usr/bin/env python|${python.bin}|g" ${worksrcpath}/pdb2pka/pka.py
- reinplace "s|/usr/bin/python|${python.bin}|g" ${worksrcpath}/src/psize.py
- reinplace "s|-Wl,-framework -Wl,Python -bundle|${python.lib} -bundle|g" \
- ${worksrcpath}/configure \
- ${worksrcpath}/propka/configure
- delete ${worksrcpath}/contrib
+ fs-traverse f ${worksrcpath} {
+ if {[file isfile ${f}] && [file extension ${f}] eq ".py"} {
+ reinplace -E "s,(/usr/bin/python|/usr/bin/env python),${prefix}/bin/python${python.branch},g" ${f}
+ }
+ }
}
-configure.args --with-max-atoms="1000000" --without-url --with-python=${python.bin}
-pre-configure {
- configure.args-append -with-f77=${configure.f77}
+
+build.cmd ${prefix}/bin/python${python.branch} scons/scons.py
+build.target
+build.args BUILD_PDB2PKA=True
+
+test.run yes
+test.cmd ${prefix}/bin/python${python.branch} scons/scons.py
+test.target complete-test
+
+pre-destroot {
+ fs-traverse f ${worksrcpath} {
+ if {[file isfile ${f}] && [file extension ${f}] eq ".pyc"} {
+ delete ${f}
+ }
+ }
+ foreach f {build_config.py pdb2pqr.py.in tools SConscript-error.py SConscript-install.py SConscript-main.py SConscript scons site_scons} {
+ delete ${worksrcpath}/${f}
+ }
}
destroot {
- system "find ${worksrcpath} -name '*.o' -delete"
- file mkdir ${destroot}${prefix}/share/{name}
move ${worksrcpath} ${destroot}${prefix}/share/${name}
system "echo '#!/bin/zsh -f' >| ${destroot}${prefix}/bin/pdb2pqr"
system "echo '${prefix}/share/${name}/pdb2pqr.py \"\$@\"' >> ${destroot}${prefix}/bin/pdb2pqr"
file attributes ${destroot}${prefix}/bin/pdb2pqr -permissions a+x
+ file attributes ${destroot}${prefix}/share/${name}/propka30/propka.py -permissions a+x
system "echo '#!/bin/zsh -f' >| ${destroot}${prefix}/bin/propka"
- system "echo '${prefix}/share/${name}/propka/propka \"\$@\"' >> ${destroot}${prefix}/bin/propka"
+ system "echo '${prefix}/share/${name}/propka30/propka.py \"\$@\"' >> ${destroot}${prefix}/bin/propka"
file attributes ${destroot}${prefix}/bin/propka -permissions a+x
}
universal_variant no
-
-set gcc_versions {4.5 4.6 4.7 4.8 4.9}
-set default_fortran_variant +gcc48
-
-foreach ver ${gcc_versions} {
- set ver_no_dot [join [split ${ver} "."] ""]
-
- set variant_line {variant gcc${ver_no_dot} description "build with gfortran from gcc${ver_no_dot}"}
-
- foreach over ${gcc_versions} {
- if {${ver} == ${over}} {
- continue
- }
-
- set over_no_dot [join [split ${over} "."] ""]
- append variant_line " conflicts gcc${over_no_dot}"
- }
- append variant_line { {}}
-
- eval $variant_line
-
- if {[variant_isset gcc${ver_no_dot}]} {
- if {${default_fortran_variant} != "+gcc${ver_no_dot}"} {
- set default_fortran_variant ""
- }
- }
-}
-
-if {${default_fortran_variant} != ""} {
- default_variants-append "${default_fortran_variant}"
-}
-
-foreach ver ${gcc_versions} {
- set ver_no_dot [join [split ${ver} "."] ""]
-
- if {[variant_isset gcc${ver_no_dot}]} {
- depends_lib-append path:lib/libgcc/libgcc_s.1.dylib:libgcc
- depends_build-append port:gcc${ver_no_dot}
-
- configure.fc ${prefix}/bin/gfortran-mp-${ver}
- configure.f77 ${prefix}/bin/gfortran-mp-${ver}
- configure.f90 ${prefix}/bin/gfortran-mp-${ver}
- }
-}
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