Closed Pilibeibei closed 3 years ago
burkholderab
commented
3 years ago It looks like this issue is due to an attempt to install and import a version of the Click package that is not compatible with python 2.7. I've updated the setup.py script to require Click >=6.0 and <= 7.1.12. Try downloading a fresh copy and running the install script again.
Pilibeibei
commented
3 years ago Thanks for the quick reply. I have successfully installed. However when run the code I have an error called "ConfigParser.MissingSectionHeaderError: File contains no section headers." see below details.
Traceback (most recent call last):
File "/usr/local/bin/ROTLA", line 11, in
burkholderab
commented
3 years ago This looks like an issue with the contents of paths.cfg. Make sure it looks similar to the example below and includes the header line in square brackets and the full path to your blat executable:
[paths] blat = /home/abc/blatSrc/blat
Note that the installer places paths.cfg in ~/.local/lib/python2.7/site-packages/ROTLA-0.1.0-py2.7.egg/config/. You can either edit the file there, or edit the copy in the ROTLA source folder and re-run the setup script.
From: Pilibeibei notifications@github.com Sent: Thursday, December 17, 2020 10:17 PM To: NIEHS/ROTLA ROTLA@noreply.github.com Cc: Burkholder, Adam (NIH/NIEHS) [E] adam.burkholder@nih.gov; Comment comment@noreply.github.com Subject: Re: [NIEHS/ROTLA] invalid syntax when installation of ROTLA (#1)
Thanks for the quick reply. I have successfully installed. However when run the code I have an error called "ConfigParser.MissingSectionHeaderError: File contains no section headers." see below details.
Traceback (most recent call last): File "/usr/local/bin/ROTLA", line 11, in load_entry_point('ROTLA==0.1.0', 'console_scripts', 'ROTLA')() File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 489, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 2852, in load_entry_point return ep.load() File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 2443, in load return self.resolve() File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 2449, in resolve module = import(self.module_name, fromlist=['name'], level=0) File "/home/jing/.local/lib/python2.7/site-packages/ROTLA-0.1.0-py2.7.egg/ROTLA/init.py", line 15, in os.path.dirname(os.path.abspath(file)), '../config', 'paths.cfg')) File "/usr/lib/python2.7/ConfigParser.py", line 305, in read self._read(fp, filename) File "/usr/lib/python2.7/ConfigParser.py", line 512, in _read raise MissingSectionHeaderError(fpname, lineno, line) ConfigParser.MissingSectionHeaderError: File contains no section headers. file: /home/jing/.local/lib/python2.7/site-packages/ROTLA-0.1.0-py2.7.egg/ROTLA/../config/paths.cfg, line: 1 '/home/jing/bin/x86_64/\n'
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Hi, I have issue when installing the ROTLA on Ubuntu20.04VM. I have installed blat and add it to the path in the "paths.cfg" as following: /home/abc/blatSrc blat = blat
Then I run "sudo python2 setup.py install" and received the error as invalid syntax, below are the results. running install running bdist_egg running egg_info writing requirements to ROTLA.egg-info/requires.txt writing ROTLA.egg-info/PKG-INFO writing top-level names to ROTLA.egg-info/top_level.txt writing dependency_links to ROTLA.egg-info/dependency_links.txt writing entry points to ROTLA.egg-info/entry_points.txt reading manifest file 'ROTLA.egg-info/SOURCES.txt' writing manifest file 'ROTLA.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/ROTLA copying build/lib.linux-x86_64-2.7/ROTLA/init.py -> build/bdist.linux-x86_64/egg/ROTLA copying build/lib.linux-x86_64-2.7/ROTLA/ROTLA.py -> build/bdist.linux-x86_64/egg/ROTLA copying build/lib.linux-x86_64-2.7/ROTLA/aligned_bases_from_psl.py -> build/bdist.linux-x86_64/egg/ROTLA copying build/lib.linux-x86_64-2.7/ROTLA/cli.py -> build/bdist.linux-x86_64/egg/ROTLA copying build/lib.linux-x86_64-2.7/ROTLA/compile_breakpoint_results.py -> build/bdist.linux-x86_64/egg/ROTLA byte-compiling build/bdist.linux-x86_64/egg/ROTLA/init.py to init.pyc byte-compiling build/bdist.linux-x86_64/egg/ROTLA/ROTLA.py to ROTLA.pyc byte-compiling build/bdist.linux-x86_64/egg/ROTLA/aligned_bases_from_psl.py to aligned_bases_from_psl.pyc byte-compiling build/bdist.linux-x86_64/egg/ROTLA/cli.py to cli.pyc byte-compiling build/bdist.linux-x86_64/egg/ROTLA/compile_breakpoint_results.py to compile_breakpoint_results.pyc installing package data to build/bdist.linux-x86_64/egg running install_data creating build/bdist.linux-x86_64/egg/config copying paths.cfg -> build/bdist.linux-x86_64/egg/config creating build/bdist.linux-x86_64/egg/EGG-INFO copying ROTLA.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying ROTLA.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying ROTLA.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying ROTLA.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying ROTLA.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO copying ROTLA.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying ROTLA.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO creating 'dist/ROTLA-0.1.0-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing ROTLA-0.1.0-py2.7.egg removing '/usr/local/lib/python2.7/dist-packages/ROTLA-0.1.0-py2.7.egg' (and everything under it) creating /usr/local/lib/python2.7/dist-packages/ROTLA-0.1.0-py2.7.egg Extracting ROTLA-0.1.0-py2.7.egg to /usr/local/lib/python2.7/dist-packages ROTLA 0.1.0 is already the active version in easy-install.pth Installing ROTLA script to /usr/local/bin
Installed /usr/local/lib/python2.7/dist-packages/ROTLA-0.1.0-py2.7.egg Processing dependencies for ROTLA==0.1.0 Searching for Click>=6.0 Reading https://pypi.org/simple/Click/ Downloading https://files.pythonhosted.org/packages/60/e2/9c9b456c0ddaa1268f320bc2f739f1598290f5cf3acf8d65e2c36fde8afe/click-8.0.0a1.tar.gz#sha256=e4315a188403c0258bbc4a4e31863e48fc301c4e95b8007a8eeda0391158df13 Best match: click 8.0.0a1 Processing click-8.0.0a1.tar.gz Writing /tmp/easy_install-84T0Yf/click-8.0.0a1/setup.cfg Running click-8.0.0a1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-84T0Yf/click-8.0.0a1/egg-dist-tmp-cERIyn Traceback (most recent call last): File "setup.py", line 46, in
data_files=[('config', ['paths.cfg'])],
File "/usr/lib/python2.7/dist-packages/setuptools/init.py", line 145, in setup
return distutils.core.setup(**attrs)
File "/usr/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()
File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/usr/lib/python2.7/dist-packages/setuptools/command/install.py", line 67, in run
self.do_egg_install()
File "/usr/lib/python2.7/dist-packages/setuptools/command/install.py", line 117, in do_egg_install
cmd.run(show_deprecation=False)
File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 449, in run
self.easy_install(spec, not self.no_deps)
File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 691, in easy_install
return self.install_item(None, spec, tmpdir, deps, True)
File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 738, in install_item
self.process_distribution(spec, dist, deps)
File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 783, in process_distribution
[requirement], self.local_index, self.easy_install
File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 782, in resolve
replace_conflicting=replace_conflicting
File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 1065, in best_match
return self.obtain(req, installer)
File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 1077, in obtain
return installer(requirement)
File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 710, in easy_install
return self.install_item(spec, dist.location, tmpdir, deps)
File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 736, in install_item
dists = self.install_eggs(spec, download, tmpdir)
File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 921, in install_eggs
return self.build_and_install(setup_script, setup_base)
File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 1189, in build_and_install
self.run_setup(setup_script, setup_base, args)
File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 1175, in run_setup
run_setup(setup_script, args)
File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", line 253, in run_setup
raise
File "/usr/lib/python2.7/contextlib.py", line 35, in exit
self.gen.throw(type, value, traceback)
File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", line 195, in setup_context
yield
File "/usr/lib/python2.7/contextlib.py", line 35, in exit
self.gen.throw(type, value, traceback)
File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", line 166, in save_modules
saved_exc.resume()
File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", line 141, in resume
six.reraise(type, exc, self._tb)
File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", line 154, in save_modules
yield saved
File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", line 195, in setup_context
yield
File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", line 250, in run_setup
_execfile(setup_script, ns)
File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", line 45, in _execfile
exec(code, globals, locals)
File "/tmp/easy_install-84T0Yf/click-8.0.0a1/setup.py", line 3, in
File "/usr/lib/python2.7/dist-packages/setuptools/init.py", line 145, in setup return distutils.core.setup(**attrs) File "/usr/lib/python2.7/distutils/core.py", line 124, in setup dist.parse_config_files() File "/usr/lib/python2.7/dist-packages/setuptools/dist.py", line 702, in parse_config_files ignore_option_errors=ignore_option_errors) File "/usr/lib/python2.7/dist-packages/setuptools/config.py", line 121, in parse_configuration meta.parse() File "/usr/lib/python2.7/dist-packages/setuptools/config.py", line 426, in parse section_parser_method(section_options) File "/usr/lib/python2.7/dist-packages/setuptools/config.py", line 399, in parse_section self[name] = value File "/usr/lib/python2.7/dist-packages/setuptools/config.py", line 184, in setitem value = parser(value) File "/usr/lib/python2.7/dist-packages/setuptools/config.py", line 515, in _parse_version version = self._parse_attr(value, self.package_dir) File "/usr/lib/python2.7/dist-packages/setuptools/config.py", line 349, in _parse_attr module = import_module(module_name) File "/usr/lib/python2.7/importlib/init.py", line 37, in import_module import(name) File "/tmp/easy_install-84T0Yf/click-8.0.0a1/src/click/init.py", line 7, in
File "/tmp/easy_install-84T0Yf/click-8.0.0a1/src/click/core.py", line 91
f"{hint}. Command {base_command.name!r} is set to chain and"
^
SyntaxError: invalid syntax