diff options
Diffstat (limited to 'var')
3 files changed, 130 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/autodock-vina/main.patch b/var/spack/repos/builtin/packages/autodock-vina/main.patch new file mode 100644 index 0000000000..aafd780f64 --- /dev/null +++ b/var/spack/repos/builtin/packages/autodock-vina/main.patch @@ -0,0 +1,29 @@ +--- autodock_vina_1_1_2/src/main/main.cpp 2011-05-11 15:35:00.000000000 -0500 ++++ autodock_vina_1_1_2/src/main/main.cpp 2017-09-11 10:06:44.939452217 -0500 +@@ -47,7 +47,7 @@ + using boost::filesystem::path;
+
+ path make_path(const std::string& str) {
+- return path(str, boost::filesystem::native);
++ return path(str);
+ }
+
+ void doing(int verbosity, const std::string& str, tee& log) {
+@@ -661,7 +661,7 @@ + cpu, seed, verbosity, max_modes_sz, energy_range, log);
+ }
+ catch(file_error& e) {
+- std::cerr << "\n\nError: could not open \"" << e.name.native_file_string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
++ std::cerr << "\n\nError: could not open \"" << e.name.filename() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
+ return 1;
+ }
+ catch(boost::filesystem::filesystem_error& e) {
+@@ -673,7 +673,7 @@ + return 1;
+ }
+ catch(parse_error& e) {
+- std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.native_file_string() << "\": " << e.reason << '\n';
++ std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.filename() << "\": " << e.reason << '\n';
+ return 1;
+ }
+ catch(std::bad_alloc&) {
diff --git a/var/spack/repos/builtin/packages/autodock-vina/package.py b/var/spack/repos/builtin/packages/autodock-vina/package.py new file mode 100644 index 0000000000..082974aa6a --- /dev/null +++ b/var/spack/repos/builtin/packages/autodock-vina/package.py @@ -0,0 +1,72 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * +from shutil import copyfile +from shutil import copymode +import sys + + +class AutodockVina(MakefilePackage): + """AutoDock Vina is an open-source program for doing molecular docking""" + + homepage = "http://vina.scripps.edu/" + url = "http://vina.scripps.edu/download/autodock_vina_1_1_2.tgz" + + version('1_1_2', 'b467b71ee77dd155b65b1c5364e4220f') + + depends_on('boost@1.65.0') + + # Replacing depecrated function call of boost with current function call + patch('main.patch') + patch('split.patch') + + @property + def build_directory(self): + if sys.platform == "darwin": + return join_path('build', 'mac', 'release') + else: + return join_path('build', 'linux', 'release') + + def edit(self, spec, prefix): + with working_dir(self.build_directory): + makefile = FileFilter('Makefile') + makefile.filter('BOOST_INCLUDE = .*', 'BOOST_INCLUDE = %s' % + self.spec['boost'].prefix.include) + makefile.filter('C_PLATFORM=.*', 'C_PLATFORM=-pthread') + makefile.filter('GPP=.*', 'GPP=%s' % spack_cc) + mcp = FileFilter('../../makefile_common') + mcp.filter('LIBS = ', 'LIBS = -l stdc++ -lm ') + + def build(self, spec, prefix): + with working_dir(self.build_directory): + make() + + def install(self, spec, prefix): + with working_dir(self.build_directory): + mkdirp(prefix.bin) + copyfile("vina", join_path(prefix.bin, "vina")) + copymode("vina", join_path(prefix.bin, "vina")) + copyfile("vina_split", join_path(prefix.bin, "vina_split")) + copymode("vina_split", join_path(prefix.bin, "vina_split")) diff --git a/var/spack/repos/builtin/packages/autodock-vina/split.patch b/var/spack/repos/builtin/packages/autodock-vina/split.patch new file mode 100644 index 0000000000..e369d62216 --- /dev/null +++ b/var/spack/repos/builtin/packages/autodock-vina/split.patch @@ -0,0 +1,29 @@ +--- autodock_vina_1_1_2/src/split/split.cpp 2011-05-11 15:35:00.000000000 -0500 ++++ autodock_vina_1_1_2/src/split/split.cpp 2017-09-11 10:06:44.933452243 -0500 +@@ -38,7 +38,7 @@ + using boost::filesystem::path;
+
+ path make_path(const std::string& str) {
+- return path(str, boost::filesystem::native);
++ return path(str);
+ }
+
+ std::string default_prefix(const std::string& input_name, const std::string& add) {
+@@ -208,7 +208,7 @@ + write_multimodel_pdbqt(tmp, ligand_prefix, flex_prefix);
+ }
+ catch(file_error& e) {
+- std::cerr << "\n\nError: could not open \"" << e.name.native_file_string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
++ std::cerr << "\n\nError: could not open \"" << e.name.filename() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
+ return 1;
+ }
+ catch(boost::filesystem::filesystem_error& e) {
+@@ -220,7 +220,7 @@ + return 1;
+ }
+ catch(parse_error& e) {
+- std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.native_file_string() << "\": " << e.reason << '\n';
++ std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.filename() << "\": " << e.reason << '\n';
+ return 1;
+ }
+ catch(std::bad_alloc&) {
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