1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/78a2fa5ee8b8/ Changeset: 78a2fa5ee8b8 User: dan Date: 2014-04-29 18:13:01 Summary: Fix for setting environment paths when using setup_virutalenv. Affected #: 1 file
diff -r 9469c1d11af520686d6c0e934146dbdab05995a8 -r 78a2fa5ee8b82011c09a152c5be5334eb14d8ded lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py @@ -1158,20 +1158,15 @@ full_setup_command = "%s; %s; %s" % ( setup_command, activate_command, install_command ) return_code = install_environment.handle_command( app, tool_dependency, install_dir, full_setup_command ) if return_code: + log.error( "Failed to do setup_virtualenv install, exit code='%s'", return_code ) + # would it be better to try to set env variables anway, instead of returning here? return tool_dependency, None, None - # Use raw strings so that python won't automatically unescape the quotes before passing the command - # to subprocess.Popen. - site_packages_command = \ - r"""%s -c 'import os, sys; print os.path.join(sys.prefix, "lib", "python" + sys.version[:3], "site-packages")'""" % \ - os.path.join( venv_directory, "bin", "python" ) - output = install_environment.handle_command( app, tool_dependency, install_dir, site_packages_command, return_output=True ) - if output.return_code: - return tool_dependency, None, None - if not os.path.exists( output.stdout ): - log.debug( "virtualenv's site-packages directory '%s' does not exist", output.stdout ) - return tool_dependency, None, None - env_file_builder.append_line( name="PYTHONPATH", action="prepend_to", value=output.stdout ) + site_packages_directory, site_packages_directory_list = self.__get_site_packages_directory( install_environment, app, tool_dependency, install_dir, python_cmd, venv_directory ) env_file_builder.append_line( name="PATH", action="prepend_to", value=os.path.join( venv_directory, "bin" ) ) + if site_packages_directory is None: + log.error( "virtualenv's site-packages directory '%s' does not exist", site_packages_directory_list ) + else: + env_file_builder.append_line( name="PYTHONPATH", action="prepend_to", value=site_packages_directory ) # The caller should check the status of the returned tool_dependency since this function does nothing # with the return_code. return_code = env_file_builder.return_code @@ -1203,6 +1198,34 @@ action_dict[ 'python' ] = action_elem.get( 'python', 'python' ) return action_dict
+ def __get_site_packages_directory( self, install_environment, app, tool_dependency, install_dir, python_cmd, venv_directory ): + lib_dir = os.path.join( venv_directory, "lib" ) + rval = os.path.join( lib_dir, python_cmd, 'site-packages' ) + site_packages_directory_list = [ rval ] + if os.path.exists( rval ): + return ( rval, site_packages_directory_list ) + for ( dirpath, dirnames, filenames ) in os.walk( lib_dir ): + for dirname in dirnames: + rval = os.path.join( lib_dir, dirname, 'site-packages' ) + site_packages_directory_list.append( rval ) + if os.path.exists( rval ): + return ( rval, site_packages_directory_list ) + break + # fall back to python call to get site packages + # FIXME: This is probably more robust?, but there is currently an issue with handling the output.stdout + # preventing the entire path from being included (it gets truncated) + # Use raw strings so that python won't automatically unescape the quotes before passing the command + # to subprocess.Popen. + for site_packages_command in [ r"""%s -c 'import site; site.getsitepackages()[0]'""" % \ + os.path.join( venv_directory, "bin", "python" ), + r"""%s -c 'import os, sys; print os.path.join( sys.prefix, "lib", "python" + sys.version[:3], "site-packages" )'""" % \ + os.path.join( venv_directory, "bin", "python" ) ]: + output = install_environment.handle_command( app, tool_dependency, install_dir, site_packages_command, return_output=True ) + site_packages_directory_list.append( output.stdout ) + if not output.return_code and os.path.exists( output.stdout ): + return ( output.stdout, site_packages_directory_list ) + return ( None, site_packages_directory_list ) + class ShellCommand( RecipeStep ):
def __init__( self ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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