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Merge pull request #698 from bgruening/pip_install

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Use setup.py for Python all installations
This commit is contained in:
John Chilton
2015-09-17 18:25:45 +01:00
parent c74cda3c60 4e063e793f
commit d717ec833d
1 changed files with 16 additions and 14 deletions
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lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
+16 -14
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@@ -1577,8 +1577,6 @@ class SetupPythonEnvironment( Download, RecipeStep ):
and returned and the installation directory (i.e., dir) will be defined and returned. If we're not
in the initial download stage, these actions will not occur, and None values will be returned for them.
Warning: easy_install is configured that it will not be install any dependency, the tool developer needs
to specify every dependency explicitly
"""
# <action type="setup_python_environment">
# <repository name="package_python_2_7" owner="bgruening">
@@ -1611,26 +1609,27 @@ class SetupPythonEnvironment( Download, RecipeStep ):
package, package_version = python_package_tup
package_path = os.path.join( install_environment.tool_shed_repository_install_dir, package )
if os.path.isfile( package_path ):
# we assume a local shipped python package
cmd = r'''PATH=$PATH:$PYTHONHOME/bin; export PATH;
export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR;
easy_install --no-deps --install-dir $INSTALL_DIR --script-dir $INSTALL_DIR/bin %s
''' % ( package_path )
# We assume a local shipped python package.
package_to_install = package_path
elif package.find( '://' ) != -1:
# We assume a URL to a python package.
url = package
package_name = url.split( '/' )[ -1 ]
checksums = python_package_tup_dict.get('checksums', {})
self.url_download( work_dir, package_name, url, extract=False, checksums=checksums )
cmd = r'''PATH=$PATH:$PYTHONHOME/bin; export PATH;
export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR;
easy_install --no-deps --install-dir $INSTALL_DIR --script-dir $INSTALL_DIR/bin %s
''' % ( package_name )
package_to_install = os.path.join( work_dir, package_name )
else:
# pypi support is currently not working - pip can not install wheels into user specified directories
pass
# pypi can be implemented or for > python3.4 we can use the build-in system
archive = CompressedFile(package_to_install)
uncompressed_path = archive.extract( work_dir )
cmd = r'''PATH=$PYTHONHOME/bin:$PATH; export PATH;
mkdir -p $INSTALL_DIR/lib/python;
export PYTHONPATH=$INSTALL_DIR/lib/python:$PYTHONPATH;
cd %s;
python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
''' % ( uncompressed_path )
cmd = install_environment.build_command( basic_util.evaluate_template( cmd, install_environment ) )
return_code = install_environment.handle_command( tool_dependency=tool_dependency,
cmd=cmd,
@@ -1644,6 +1643,9 @@ class SetupPythonEnvironment( Download, RecipeStep ):
env_file_builder.append_line( name="PYTHONPATH",
action="prepend_to",
value=os.path.join( install_environment.install_dir, 'lib', 'python') )
env_file_builder.append_line( name="PYTHONPATH",
action="prepend_to",
value=os.path.join( install_environment.install_dir) )
env_file_builder.append_line( name="PATH",
action="prepend_to",
value=os.path.join( install_environment.install_dir, 'bin' ) )