def main_non_archive(args):
# validation
if not args.galaxy_root:
raise ValueError(
'in non-archive mode the galaxy root must be specified')
if not args.tools_subdir:
raise ValueError(
'in non-archive mode the tools subdirectory must be specified')
# get the module names
module_names = meta.get_module_names(
args.manifest, args.create_all, args.create_tagged)
# create the python subtree
tools_subdir_path = os.path.join(
args.galaxy_root, 'tools', args.tools_subdir)
meta.add_python_files(module_names, tools_subdir_path)
shutil.copyfile('galaxy_format_tweak.py',
os.path.join(tools_subdir_path, 'galaxy_format_tweak.py'))
# create the galaxy xml interface files
xml_filenames, import_errors = add_xml_files(args.galaxy_root,
module_names, args.short_length, args.tools_subdir)
for e in import_errors:
print e
# create the toolbox xml pointing to the installed xmls
toolbox_pathname = os.path.join(args.galaxy_root, args.tool_conf)
section_name = args.tools_subdir
section_id = args.tools_subdir
toolbox_xml = get_toolbox_xml(section_name, section_id,
args.tools_subdir, xml_filenames)
with open(toolbox_pathname, 'wt') as fout:
fout.write(toolbox_xml)
def main_non_archive(args):
# validation
if not args.galaxy_root:
raise ValueError(
'in non-archive mode the galaxy root must be specified')
if not args.tools_subdir:
raise ValueError(
'in non-archive mode the tools subdirectory must be specified')
# get the module names
module_names = meta.get_module_names(args.manifest, args.create_all,
args.create_tagged)
# create the python subtree
tools_subdir_path = os.path.join(args.galaxy_root, 'tools',
args.tools_subdir)
meta.add_python_files(module_names, tools_subdir_path)
shutil.copyfile('galaxy_format_tweak.py',
os.path.join(tools_subdir_path, 'galaxy_format_tweak.py'))
# create the galaxy xml interface files
xml_filenames, import_errors = add_xml_files(args.galaxy_root,
module_names,
args.short_length,
args.tools_subdir)
for e in import_errors:
print e
# create the toolbox xml pointing to the installed xmls
toolbox_pathname = os.path.join(args.galaxy_root, args.tool_conf)
section_name = args.tools_subdir
section_id = args.tools_subdir
toolbox_xml = get_toolbox_xml(section_name, section_id, args.tools_subdir,
xml_filenames)
with open(toolbox_pathname, 'wt') as fout:
fout.write(toolbox_xml)
def main(args):
module_names = meta.get_module_names(
args.manifest, args.create_all, args.create_tagged)
module_deps, const_deps = meta.get_module_and_const_deps(module_names)
print 'module deps:'
for module_dep in module_deps:
print module_dep
print
print 'const deps:'
for const_dep in const_deps:
print const_dep
def main(args):
module_names = meta.get_module_names(args.manifest, args.create_all,
args.create_tagged)
module_deps, const_deps = meta.get_module_and_const_deps(module_names)
print 'module deps:'
for module_dep in module_deps:
print module_dep
print
print 'const deps:'
for const_dep in const_deps:
print const_dep
def main_archive(args):
# validation
if args.galaxy_root:
raise ValueError(
'in archive mode the galaxy root must not be specified')
if args.tools_subdir:
raise ValueError(
'in archive mode the tools subdirectory must not be specified')
# define the archive extension and the compression command
archive_extension = '.tar.bz2'
archive_prefix = os.path.basename(args.suite_archive.rstrip('/'))
archive_name = archive_prefix + archive_extension
archive_cmd = ['tar', 'cjvf', archive_name, args.suite_archive]
# delete the suite directory and archive if they exist
try:
shutil.rmtree(args.suite_archive)
os.remove(archive_name)
except OSError as e:
pass
# get the module names
module_names = meta.get_module_names(args.manifest, args.create_all,
args.create_tagged)
# create the empty suite directory
os.makedirs(args.suite_archive)
# add the python files
meta.add_python_files(module_names, args.suite_archive)
shutil.copyfile('galaxy_format_tweak.py',
os.path.join(args.suite_archive, 'galaxy_format_tweak.py'))
# create the galaxy xml interface files
mod_infos, import_errors = add_xml_archive_files(module_names,
args.short_length,
args.suite_archive)
for e in import_errors:
print e
# create the toolbox xml pointing to the installed xmls
config_pathname = os.path.join(args.suite_archive, 'suite_config.xml')
config_xml = get_suite_config_xml(mod_infos, archive_prefix)
with open(config_pathname, 'wt') as fout:
fout.write(config_xml)
# use subprocess instead of tarfile to create the tgz
subprocess.call(archive_cmd)
def main_archive(args):
# validation
if args.galaxy_root:
raise ValueError(
'in archive mode the galaxy root must not be specified')
if args.tools_subdir:
raise ValueError(
'in archive mode the tools subdirectory must not be specified')
# define the archive extension and the compression command
archive_extension = '.tar.bz2'
archive_prefix = os.path.basename(args.suite_archive.rstrip('/'))
archive_name = archive_prefix + archive_extension
archive_cmd = ['tar', 'cjvf', archive_name, args.suite_archive]
# delete the suite directory and archive if they exist
try:
shutil.rmtree(args.suite_archive)
os.remove(archive_name)
except OSError as e:
pass
# get the module names
module_names = meta.get_module_names(
args.manifest, args.create_all, args.create_tagged)
# create the empty suite directory
os.makedirs(args.suite_archive)
# add the python files
meta.add_python_files(module_names, args.suite_archive)
shutil.copyfile('galaxy_format_tweak.py',
os.path.join(args.suite_archive, 'galaxy_format_tweak.py'))
# create the galaxy xml interface files
mod_infos, import_errors = add_xml_archive_files(
module_names, args.short_length, args.suite_archive)
for e in import_errors:
print e
# create the toolbox xml pointing to the installed xmls
config_pathname = os.path.join(args.suite_archive, 'suite_config.xml')
config_xml = get_suite_config_xml(mod_infos, archive_prefix)
with open(config_pathname, 'wt') as fout:
fout.write(config_xml)
# use subprocess instead of tarfile to create the tgz
subprocess.call(archive_cmd)
def main(args):
# check for flag conflicts
if args.deploy and args.make_installer:
raise ValueError(
'the "deploy" and "make_installer" flags are incompatible')
# initialize the mobyle category information
cat_info = mobyle.CategoryInfo(args.show_io_types, args.show_tags,
args.universal_category)
# get the module names
module_names = meta.get_module_names(args.manifest, args.create_all,
args.create_tagged)
# define the environment on the target server
auto_path = os.path.join(args.target, 'auto.py')
env_info = mobenv.create_environment_info(auto_path, args.python_path,
args.mobyle_core,
args.mobyle_version)
if args.make_installer:
create_installer(args, cat_info, env_info, module_names)
else:
# create the python subtree
meta.add_python_files(module_names, args.target)
# create the mobyle xml interface files
import_errors = mobyle.add_xml_files(cat_info, env_info, module_names,
args.short_length,
env_info.get_xml_dir(),
args.runbsub)
for e in import_errors:
print e
if args.clean:
cmd = env_info.get_clean_command()
subprocess.call(cmd)
if args.index:
cmd = env_info.get_index_command()
subprocess.call(cmd)
if args.deploy:
cmd = env_info.get_deploy_command()
subprocess.call(cmd)
def main(args):
# check for flag conflicts
if args.deploy and args.make_installer:
raise ValueError(
'the "deploy" and "make_installer" flags are incompatible')
# initialize the mobyle category information
cat_info = mobyle.CategoryInfo(
args.show_io_types, args.show_tags, args.universal_category)
# get the module names
module_names = meta.get_module_names(
args.manifest, args.create_all, args.create_tagged)
# define the environment on the target server
auto_path = os.path.join(args.target, 'auto.py')
env_info = mobenv.create_environment_info(
auto_path, args.python_path,
args.mobyle_core, args.mobyle_version)
if args.make_installer:
create_installer(args, cat_info, env_info, module_names)
else:
# create the python subtree
meta.add_python_files(module_names, args.target)
# create the mobyle xml interface files
import_errors = mobyle.add_xml_files(
cat_info, env_info,
module_names, args.short_length, env_info.get_xml_dir(),
args.runbsub)
for e in import_errors:
print e
if args.clean:
cmd = env_info.get_clean_command()
subprocess.call(cmd)
if args.index:
cmd = env_info.get_index_command()
subprocess.call(cmd)
if args.deploy:
cmd = env_info.get_deploy_command()
subprocess.call(cmd)
