def install_virtualenv( app, venv_dir ):
if not os.path.exists( venv_dir ):
with make_tmp_dir() as work_dir:
downloaded_filename = VIRTUALENV_URL.rsplit('/', 1)[-1]
downloaded_file_path = common_util.url_download( work_dir, downloaded_filename, VIRTUALENV_URL )
if common_util.istar( downloaded_file_path ):
common_util.extract_tar( downloaded_file_path, work_dir )
dir = common_util.tar_extraction_directory( work_dir, downloaded_filename )
else:
log.error( "Failed to download virtualenv: Downloaded file '%s' is not a tar file", downloaded_filename )
return False
full_path_to_dir = os.path.abspath( os.path.join( work_dir, dir ) )
shutil.move( full_path_to_dir, venv_dir )
return True
def install_virtualenv(app, venv_dir):
if not os.path.exists(venv_dir):
with make_tmp_dir() as work_dir:
downloaded_filename = VIRTUALENV_URL.rsplit('/', 1)[-1]
downloaded_file_path = common_util.url_download(
work_dir, downloaded_filename, VIRTUALENV_URL)
if common_util.istar(downloaded_file_path):
common_util.extract_tar(downloaded_file_path, work_dir)
dir = common_util.tar_extraction_directory(
work_dir, downloaded_filename)
else:
log.error(
"Failed to download virtualenv: Downloaded file '%s' is not a tar file",
downloaded_filename)
return False
full_path_to_dir = os.path.abspath(os.path.join(work_dir, dir))
shutil.move(full_path_to_dir, venv_dir)
return True
def install_and_build_package( app, tool_dependency, actions_dict ):
"""Install a Galaxy tool dependency package either via a url or a mercurial or git clone command."""
sa_session = app.model.context.current
install_dir = actions_dict[ 'install_dir' ]
package_name = actions_dict[ 'package_name' ]
#download_url = actions_dict.get( 'download_url', None )
#clone_cmd = actions_dict.get( 'clone_cmd', None )
actions = actions_dict.get( 'actions', None )
if actions:
with make_tmp_dir() as work_dir:
with lcd( work_dir ):
# The first action in the list of actions will be the one that defines the installation process. There
# are currently only two supported processes; download_by_url and clone via a "shell_command" action type.
action_type, action_dict = actions[ 0 ]
if action_type == 'download_by_url':
# <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
url = action_dict[ 'url' ]
downloaded_filename = os.path.split( url )[ -1 ]
downloaded_file_path = common_util.url_download( work_dir, downloaded_filename, url )
if common_util.istar( downloaded_file_path ):
common_util.extract_tar( downloaded_file_path, work_dir )
dir = common_util.tar_extraction_directory( work_dir, downloaded_filename )
else:
dir = work_dir
elif action_type == 'shell_command':
# <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action>
clone_cmd = action_dict[ 'command' ]
output = local( clone_cmd, capture=True )
log_results( clone_cmd, output, os.path.join( install_dir, INSTALLATION_LOG ) )
if output.return_code:
tool_dependency.status = app.model.ToolDependency.installation_status.ERROR
tool_dependency.error_message = str( output.stderr )
sa_session.add( tool_dependency )
sa_session.flush()
return
dir = package_name
if not os.path.exists( dir ):
os.makedirs( dir )
# The package has been down-loaded, so we can now perform all of the actions defined for building it.
with lcd( dir ):
for action_tup in actions[ 1: ]:
action_type, action_dict = action_tup
current_dir = os.path.abspath( os.path.join( work_dir, dir ) )
if action_type == 'move_directory_files':
common_util.move_directory_files( current_dir=current_dir,
source_dir=os.path.join( action_dict[ 'source_directory' ] ),
destination_dir=os.path.join( action_dict[ 'destination_directory' ] ) )
elif action_type == 'move_file':
common_util.move_file( current_dir=current_dir,
source=os.path.join( action_dict[ 'source' ] ),
destination_dir=os.path.join( action_dict[ 'destination' ] ) )
elif action_type == 'set_environment':
# Currently the only action supported in this category is "environment_variable".
env_var_dict = action_dict[ 'environment_variable' ]
env_var_name = env_var_dict[ 'name' ]
env_var_action = env_var_dict[ 'action' ]
env_var_value = env_var_dict[ 'value' ]
if env_var_action == 'prepend_to':
changed_value = '%s:$%s' % ( env_var_value, env_var_name )
elif env_var_action == 'set_to':
changed_value = '%s' % env_var_value
elif env_var_action == 'append_to':
changed_value = '$%s:%s' % ( env_var_name, env_var_value )
cmd = "echo '%s=%s; export %s' > %s/env.sh;chmod +x %s/env.sh" % ( env_var_name,
changed_value,
env_var_name,
install_dir,
install_dir )
output = local( cmd, capture=True )
log_results( cmd, output, os.path.join( install_dir, INSTALLATION_LOG ) )
if output.return_code:
tool_dependency.status = app.model.ToolDependency.installation_status.ERROR
tool_dependency.error_message = str( output.stderr )
sa_session.add( tool_dependency )
sa_session.flush()
return
elif action_type == 'shell_command':
action = action_dict[ 'command' ]
with settings( warn_only=True ):
output = local( action, capture=True )
log_results( action, output, os.path.join( install_dir, INSTALLATION_LOG ) )
if output.return_code:
tool_dependency.status = app.model.ToolDependency.installation_status.ERROR
tool_dependency.error_message = str( output.stderr )
sa_session.add( tool_dependency )
sa_session.flush()
return
def install_and_build_package( app, tool_dependency, actions_dict ):
"""Install a Galaxy tool dependency package either via a url or a mercurial or git clone command."""
sa_session = app.model.context.current
install_dir = actions_dict[ 'install_dir' ]
package_name = actions_dict[ 'package_name' ]
actions = actions_dict.get( 'actions', None )
filtered_actions = []
if actions:
with make_tmp_dir() as work_dir:
with lcd( work_dir ):
# The first action in the list of actions will be the one that defines the installation process. There
# are currently only two supported processes; download_by_url and clone via a "shell_command" action type.
action_type, action_dict = actions[ 0 ]
if action_type == 'download_by_url':
# Eliminate the download_by_url action so remaining actions can be processed correctly.
filtered_actions = actions[ 1: ]
url = action_dict[ 'url' ]
if 'target_filename' in action_dict:
downloaded_filename = action_dict[ 'target_filename' ]
else:
downloaded_filename = os.path.split( url )[ -1 ]
downloaded_file_path = common_util.url_download( work_dir, downloaded_filename, url )
if common_util.istar( downloaded_file_path ):
# <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
common_util.extract_tar( downloaded_file_path, work_dir )
dir = common_util.tar_extraction_directory( work_dir, downloaded_filename )
elif common_util.iszip( downloaded_file_path ):
# <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-tools-1.56.zip</action>
zip_archive_extracted = common_util.extract_zip( downloaded_file_path, work_dir )
dir = common_util.zip_extraction_directory( work_dir, downloaded_filename )
else:
dir = work_dir
elif action_type == 'shell_command':
# <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action>
# Eliminate the shell_command clone action so remaining actions can be processed correctly.
filtered_actions = actions[ 1: ]
return_code = handle_command( app, tool_dependency, install_dir, action_dict[ 'command' ] )
if return_code:
return
dir = package_name
else:
# We're handling a complex repository dependency where we only have a set_environment tag set.
# <action type="set_environment">
# <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
# </action>
filtered_actions = [ a for a in actions ]
dir = install_dir
if not os.path.exists( dir ):
os.makedirs( dir )
# The package has been down-loaded, so we can now perform all of the actions defined for building it.
with lcd( dir ):
for action_tup in filtered_actions:
action_type, action_dict = action_tup
current_dir = os.path.abspath( os.path.join( work_dir, dir ) )
if action_type == 'make_directory':
common_util.make_directory( full_path=action_dict[ 'full_path' ] )
elif action_type == 'move_directory_files':
common_util.move_directory_files( current_dir=current_dir,
source_dir=os.path.join( action_dict[ 'source_directory' ] ),
destination_dir=os.path.join( action_dict[ 'destination_directory' ] ) )
elif action_type == 'move_file':
# TODO: Remove this hack that resets current_dir so that the pre-compiled bwa binary can be found.
# current_dir = '/Users/gvk/workspaces_2008/bwa/bwa-0.5.9'
common_util.move_file( current_dir=current_dir,
source=os.path.join( action_dict[ 'source' ] ),
destination_dir=os.path.join( action_dict[ 'destination' ] ) )
elif action_type == 'set_environment':
# Currently the only action supported in this category is "environment_variable".
env_var_dicts = action_dict[ 'environment_variable' ]
for env_var_dict in env_var_dicts:
cmd = common_util.create_or_update_env_shell_file( install_dir, env_var_dict )
return_code = handle_command( app, tool_dependency, install_dir, cmd )
if return_code:
return
elif action_type == 'shell_command':
with settings( warn_only=True ):
return_code = handle_command( app, tool_dependency, install_dir, action_dict[ 'command' ] )
if return_code:
return
def install_and_build_package(app, tool_dependency, actions_dict):
"""Install a Galaxy tool dependency package either via a url or a mercurial or git clone command."""
sa_session = app.model.context.current
install_dir = actions_dict['install_dir']
package_name = actions_dict['package_name']
actions = actions_dict.get('actions', None)
filtered_actions = []
if actions:
with make_tmp_dir() as work_dir:
with lcd(work_dir):
# The first action in the list of actions will be the one that defines the installation process. There
# are currently only two supported processes; download_by_url and clone via a "shell_command" action type.
action_type, action_dict = actions[0]
if action_type == 'download_by_url':
# Eliminate the download_by_url action so remaining actions can be processed correctly.
filtered_actions = actions[1:]
url = action_dict['url']
if 'target_filename' in action_dict:
downloaded_filename = action_dict['target_filename']
else:
downloaded_filename = os.path.split(url)[-1]
downloaded_file_path = common_util.url_download(
work_dir, downloaded_filename, url)
if common_util.istar(downloaded_file_path):
# <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
common_util.extract_tar(downloaded_file_path, work_dir)
dir = common_util.tar_extraction_directory(
work_dir, downloaded_filename)
elif common_util.iszip(downloaded_file_path):
# <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-tools-1.56.zip</action>
zip_archive_extracted = common_util.extract_zip(
downloaded_file_path, work_dir)
dir = common_util.zip_extraction_directory(
work_dir, downloaded_filename)
else:
dir = work_dir
elif action_type == 'shell_command':
# <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action>
# Eliminate the shell_command clone action so remaining actions can be processed correctly.
filtered_actions = actions[1:]
return_code = handle_command(app, tool_dependency,
install_dir,
action_dict['command'])
if return_code:
return
dir = package_name
else:
# We're handling a complex repository dependency where we only have a set_environment tag set.
# <action type="set_environment">
# <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
# </action>
filtered_actions = [a for a in actions]
dir = install_dir
if not os.path.exists(dir):
os.makedirs(dir)
# The package has been down-loaded, so we can now perform all of the actions defined for building it.
with lcd(dir):
for action_tup in filtered_actions:
action_type, action_dict = action_tup
current_dir = os.path.abspath(
os.path.join(work_dir, dir))
if action_type == 'make_directory':
common_util.make_directory(
full_path=action_dict['full_path'])
elif action_type == 'move_directory_files':
common_util.move_directory_files(
current_dir=current_dir,
source_dir=os.path.join(
action_dict['source_directory']),
destination_dir=os.path.join(
action_dict['destination_directory']))
elif action_type == 'move_file':
# TODO: Remove this hack that resets current_dir so that the pre-compiled bwa binary can be found.
# current_dir = '/Users/gvk/workspaces_2008/bwa/bwa-0.5.9'
common_util.move_file(
current_dir=current_dir,
source=os.path.join(action_dict['source']),
destination_dir=os.path.join(
action_dict['destination']))
elif action_type == 'set_environment':
# Currently the only action supported in this category is "environment_variable".
env_var_dicts = action_dict['environment_variable']
for env_var_dict in env_var_dicts:
cmd = common_util.create_or_update_env_shell_file(
install_dir, env_var_dict)
return_code = handle_command(
app, tool_dependency, install_dir, cmd)
if return_code:
return
elif action_type == 'shell_command':
with settings(warn_only=True):
return_code = handle_command(
app, tool_dependency, install_dir,
action_dict['command'])
if return_code:
return