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 create_installer(args, cat_info, env_info, module_names):
"""
Overwrite a staging subtree of the current directory.
The idea it to tgz this directory and send it to the target server.
On the target server it should be unzipped and extracted,
and the installer script should put everything in the correct
prespecified directories.
"""
# define the local staging directory
stage = args.make_installer
# remove the old staging directory if it exists
if os.path.isdir(stage):
shutil.rmtree(stage)
# create some directories
os.makedirs(os.path.join(stage, 'python-files'))
os.makedirs(os.path.join(stage, 'xml-files'))
# add the appropriate python files and the const data
meta.add_python_files(module_names, os.path.join(stage, 'python-files'))
# create the xml files
identifiers, import_errors = mobyle.add_xml_files(
cat_info, env_info,
module_names, args.short_length,
os.path.join(stage, 'xml-files'),
args.runbsub)
for e in import_errors:
print e
# copy the installer script
shutil.copy('install-mob-tools.py',
os.path.join(stage, 'install-mob-tools.py'))
# copy the installer script dependency
shutil.copy('mobenv.py',
os.path.join(stage, 'mobenv.py'))
# create the installer configuration
with open(os.path.join(stage, 'install-mob-tools.conf'), 'w') as fout:
print >> fout, '#', ' '.join(sys.argv)
print >> fout, '\t'.join(['auto_path', env_info.auto_path])
print >> fout, '\t'.join(['python_path', env_info.python_path])
print >> fout, '\t'.join(['mob_core', env_info.mob_core])
print >> fout, '\t'.join(['mob_version', args.mobyle_version])
# create a file with a fragment that could be added to the config
with open(os.path.join(stage, 'sys.config.fragment'), 'w') as fout:
print >> fout, '# begin autogenerated code'
print >> fout, 'my_pca_names = ['
for ident in sorted(identifiers):
print >> fout, "\t\t'%s'," % ident
print >> fout, "\t\t]"
dstring = "dict((x, 'Sys') for x in my_pca_names)"
print >> fout, 'PARTICULAR_BATCH.update(%s)' % dstring
print >> fout, '# end autogenerated code'
# use subprocess instead of tarfile to create the tgz
cmd = ['tar', 'czvf', stage + '.tgz', stage]
subprocess.call(cmd)
def create_installer(args, cat_info, env_info, module_names):
"""
Overwrite a staging subtree of the current directory.
The idea it to tgz this directory and send it to the target server.
On the target server it should be unzipped and extracted,
and the installer script should put everything in the correct
prespecified directories.
"""
# define the local staging directory
stage = args.make_installer
# remove the old staging directory if it exists
if os.path.isdir(stage):
shutil.rmtree(stage)
# create some directories
os.makedirs(os.path.join(stage, 'python-files'))
os.makedirs(os.path.join(stage, 'xml-files'))
# add the appropriate python files and the const data
meta.add_python_files(module_names, os.path.join(stage, 'python-files'))
# create the xml files
identifiers, import_errors = mobyle.add_xml_files(
cat_info, env_info, module_names, args.short_length,
os.path.join(stage, 'xml-files'), args.runbsub)
for e in import_errors:
print e
# copy the installer script
shutil.copy('install-mob-tools.py',
os.path.join(stage, 'install-mob-tools.py'))
# copy the installer script dependency
shutil.copy('mobenv.py', os.path.join(stage, 'mobenv.py'))
# create the installer configuration
with open(os.path.join(stage, 'install-mob-tools.conf'), 'w') as fout:
print >> fout, '#', ' '.join(sys.argv)
print >> fout, '\t'.join(['auto_path', env_info.auto_path])
print >> fout, '\t'.join(['python_path', env_info.python_path])
print >> fout, '\t'.join(['mob_core', env_info.mob_core])
print >> fout, '\t'.join(['mob_version', args.mobyle_version])
# create a file with a fragment that could be added to the config
with open(os.path.join(stage, 'sys.config.fragment'), 'w') as fout:
print >> fout, '# begin autogenerated code'
print >> fout, 'my_pca_names = ['
for ident in sorted(identifiers):
print >> fout, "\t\t'%s'," % ident
print >> fout, "\t\t]"
dstring = "dict((x, 'Sys') for x in my_pca_names)"
print >> fout, 'PARTICULAR_BATCH.update(%s)' % dstring
print >> fout, '# end autogenerated code'
# use subprocess instead of tarfile to create the tgz
cmd = ['tar', 'czvf', stage + '.tgz', stage]
subprocess.call(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_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)
def main(args):
with open(args.manifest) as fin:
module_names = [x.strip() for x in fin]
meta.add_python_files(module_names, args.target)
