I need to download some file from remote http:
If I use to download bz2 or pdf I have this error:
Traceback (most recent call last):
File "/home/ktule/miniconda2/envs/snakemake/lib/python3.6/site-packages/snakemake/__init__.py", line 522, in snakemake
cluster_status=cluster_status)
File "/home/ktule/miniconda2/envs/snakemake/lib/python3.6/site-packages/snakemake/workflow.py", line 586, in execute
success = scheduler.schedule()
File "/home/ktule/miniconda2/envs/snakemake/lib/python3.6/site-packages/snakemake/scheduler.py", line 283, in schedule
self.run(job)
File "/home/ktule/miniconda2/envs/snakemake/lib/python3.6/site-packages/snakemake/scheduler.py", line 300, in run
error_callback=self._error)
File "/home/ktule/miniconda2/envs/snakemake/lib/python3.6/site-packages/snakemake/executors.py", line 327, in run
job.prepare()
File "/home/ktule/miniconda2/envs/snakemake/lib/python3.6/site-packages/snakemake/jobs.py", line 523, in prepare
self.download_remote_input()
File "/home/ktule/miniconda2/envs/snakemake/lib/python3.6/site-packages/snakemake/jobs.py", line 498, in download_remote_input
f.download_from_remote()
File "/home/ktule/miniconda2/envs/snakemake/lib/python3.6/site-packages/snakemake/io.py", line 270, in download_from_remote
self.remote_object.download()
File "/home/ktule/miniconda2/envs/snakemake/lib/python3.6/site-packages/snakemake/remote/HTTP.py", line 162, in download
if not self.name.endswith(".gz") and httpr.headers["Content-Encoding"] == "gzip":
File "/home/ktule/miniconda2/envs/snakemake/lib/python3.6/site-packages/requests/structures.py", line 54, in __getitem__
return self._store[key.lower()][1]
KeyError: 'content-encoding
I use the
snakemake --version
4.6.0
and
from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider
HTTP = HTTPRemoteProvider()
rule all:
input:
HTTP.remote("http://....../tools/2015-10-somatic_variant_calling_and_denovo.pdf", keep_local=True)
output:
"2015-10-somatic_variant_calling_and_denovo.pdf"
run:
shell("mv {input} {output}")
Related
I've been trying to install bs4 and selenium from the windows powershell, and here is the error message I get :
ERROR: Exception:
Traceback (most recent call last):
File "C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pip\_internal\cli\base_command.py", line 160, in exc_logging_wrapper
status = run_func(*args)
^^^^^^^^^^^^^^^
File "C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pip\_internal\cli\req_command.py", line 247, in wrapper
return func(self, options, args)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pip\_internal\commands\install.py", line 326, in run
session = self.get_default_session(options)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pip\_internal\cli\req_command.py", line 98, in get_default_session
self._session = self.enter_context(self._build_session(options))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pip\_internal\cli\req_command.py", line 125, in _build_session
session = PipSession(
^^^^^^^^^^^
File "C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pip\_internal\network\session.py", line 343, in __init__
self.headers["User-Agent"] = user_agent()
^^^^^^^^^^^^
File "C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pip\_internal\network\session.py", line 175, in user_agent
setuptools_dist = get_default_environment().get_distribution("setuptools")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pip\_internal\metadata\importlib\_envs.py", line 188, in get_distribution
return next(matches, None)
^^^^^^^^^^^^^^^^^^^
File "C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pip\_internal\metadata\importlib\_envs.py", line 183, in <genexpr>
matches = (
^
File "C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pip\_internal\metadata\base.py", line 612, in iter_all_distributions
for dist in self._iter_distributions():
File "C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pip\_internal\metadata\importlib\_envs.py", line 176, in _iter_distributions
for dist in finder.find_eggs(location):
File "C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pip\_internal\metadata\importlib\_envs.py", line 146, in find_eggs
yield from self._find_eggs_in_zip(location)
File "C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pip\_internal\metadata\importlib\_envs.py", line 123, in _find_eggs_in_zip
from pip._vendor.pkg_resources import find_eggs_in_zip
File "C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pip\_vendor\pkg_resources\__init__.py", line 3251, in <module>
#_call_aside
^^^^^^^^^^^
File "C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pip\_vendor\pkg_resources\__init__.py", line 3235, in _call_aside
f(*args, **kwargs)
File "C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pip\_vendor\pkg_resources\__init__.py", line 3277, in _initialize_master_working_set
tuple(
File "C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pip\_vendor\pkg_resources\__init__.py", line 3278, in <genexpr>
dist.activate(replace=False)
File "C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pip\_vendor\pkg_resources\__init__.py", line 2785, in activate
declare_namespace(pkg)
File "C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pip\_vendor\pkg_resources\__init__.py", line 2284, in declare_namespace
_handle_ns(packageName, path_item)
File "C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pip\_vendor\pkg_resources\__init__.py", line 2217, in _handle_ns
loader.load_module(packageName)
File "C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pygoogle\google.py", line 113
print """PyGoogle %(__version__)s
^^^^^^^^^^^^^^^^^^^^^^^^^^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(...)?
I cannot install any pip package in my pc it returns that error
pip version is : pip 22.3.1
python version is : Python 3.11.1
Appreciate Your support .
I tried to install any pip package
You've installed a package PyGoogle which is very old (2006) and works only with Python 2. You need to uninstall it:
pip uninstall -y pygoogle
If that doesn't work — remove the directory C:\Users\T470\AppData\Local\Programs\Python\Python311\Lib\site-packages\pygoogle
Did any one face this issue while downloading the latest Anaconda3 and opened spyder?
An error ocurred while starting the kernel
The error is:
Traceback (most recent call last):
File "C:\ProgramData\Anaconda3\lib\site‑packages\spyder\plugins\ipythonconsole\plugin.py", line 1173, in create_kernel_manager_and_kernel_client
kernel_manager.start_kernel(stderr=stderr_handle, **kwargs)
File "C:\Users\user\AppData\Roaming\Python\Python37\site‑packages\jupyter_client\manager.py", line 301, in start_kernel
kernel_cmd, kw = self.pre_start_kernel(**kw)
File "C:\Users\user\AppData\Roaming\Python\Python37\site‑packages\jupyter_client\manager.py", line 248, in pre_start_kernel
self.write_connection_file()
File "C:\Users\user\AppData\Roaming\Python\Python37\site‑packages\jupyter_client\connect.py", line 474, in write_connection_file
kernel_name=self.kernel_name
File "C:\Users\user\AppData\Roaming\Python\Python37\site‑packages\jupyter_client\connect.py", line 138, in write_connection_file
with secure_write(fname) as f:
File "C:\ProgramData\Anaconda3\lib\contextlib.py", line 112, in __enter__
return next(self.gen)
File "C:\Users\user\AppData\Roaming\Python\Python37\site‑packages\jupyter_core\paths.py", line 435, in secure_write
win32_restrict_file_to_user(fname)
File "C:\Users\user\AppData\Roaming\Python\Python37\site‑packages\jupyter_core\paths.py", line 361, in win32_restrict_file_to_user
import win32api
ImportError: DLL load failed: %1 is not a valid Win32 application.
Any help will be appreciated !!
I am working with conda version 4.7.12. Running the command conda update -n base conda failed. I am getting the same result when trying to update other environments as well, but the problem seemed to start when this command failed the first time. The output is:
$ conda update -n base conda
Collecting package metadata (current_repodata.json): failed
WARNING conda.exceptions:print_unexpected_error_report(1208): KeyError(u'pkgs_dirs',)
Traceback (most recent call last):
File "/home/XXXXXX/miniconda/lib/python2.7/site-packages/conda/exceptions.py", line 1206, in print_unexpected_error_report
message_builder.append(get_main_info_str(error_report['conda_info']))
File "/home/XXXXXX/miniconda/lib/python2.7/site-packages/conda/cli/main_info.py", line 236, in get_main_info_str
info_dict['_' + key] = ('\n' + 26 * ' ').join(info_dict[key])
KeyError: u'pkgs_dirs'
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/home/XXXXXX/miniconda/lib/python2.7/site-packages/conda/exceptions.py", line 1074, in __call__
return func(*args, **kwargs)
File "/home/XXXXXX/miniconda/lib/python2.7/site-packages/conda/cli/main.py", line 84, in _main
exit_code = do_call(args, p)
File "/home/XXXXXX/miniconda/lib/python2.7/site-packages/conda/cli/conda_argparse.py", line 82, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/home/XXXXXX/miniconda/lib/python2.7/site-packages/conda/cli/main_update.py", line 20, in execute
install(args, parser, 'update')
File "/home/XXXXXX/miniconda/lib/python2.7/site-packages/conda/cli/install.py", line 265, in install
should_retry_solve=(_should_retry_unfrozen or repodata_fn != repodata_fns[-1]),
File "/home/XXXXXX/miniconda/lib/python2.7/site-packages/conda/core/solve.py", line 117, in solve_for_transaction
should_retry_solve)
File "/home/XXXXXX/miniconda/lib/python2.7/site-packages/conda/core/solve.py", line 158, in solve_for_diff
force_remove, should_retry_solve)
File "/home/XXXXXX/miniconda/lib/python2.7/site-packages/conda/core/solve.py", line 262, in solve_final_state
ssc = self._collect_all_metadata(ssc)
File "/home/XXXXXX/miniconda/lib/python2.7/site-packages/conda/common/io.py", line 88, in decorated
return f(*args, **kwds)
File "/home/XXXXXX/miniconda/lib/python2.7/site-packages/conda/core/solve.py", line 415, in _collect_all_metadata
index, r = self._prepare(prepared_specs)
File "/home/XXXXXX/miniconda/lib/python2.7/site-packages/conda/core/solve.py", line 1004, in _prepare
self.subdirs, prepared_specs, self._repodata_fn)
File "/home/XXXXXX/miniconda/lib/python2.7/site-packages/conda/core/index.py", line 250, in get_reduced_index
_supplement_index_with_system(reduced_index)
File "/home/XXXXXX/miniconda/lib/python2.7/site-packages/conda/core/index.py", line 155, in _supplement_index_with_system
cuda_version = context.cuda_version
File "/home/XXXXXX/miniconda/lib/python2.7/site-packages/conda/_vendor/auxlib/decorators.py", line 268, in new_fget
cache[inner_attname] = func(self)
File "/home/XXXXXX/miniconda/lib/python2.7/site-packages/conda/common/decorators.py", line 20, in wrapper
return func(*args, **kwargs)
File "/home/XXXXXX/miniconda/lib/python2.7/site-packages/conda/base/context.py", line 770, in cuda_version
return cuda_detect()
File "/home/XXXXXX/miniconda/lib/python2.7/site-packages/conda/common/cuda.py", line 19, in cuda_detect
system = platform.system()
AttributeError: 'module' object has no attribute 'system'
`$ /home/XXXXXX/miniconda/bin/conda update -n base conda`
environment variables:
conda info could not be constructed.
KeyError(u'pkgs_dirs',)
An unexpected error has occurred. Conda has prepared the above report.
I have two files named as experiment.py and low_dim_cython.pyx. I am using python 3.4 in PyCharm. In experiment.py, I tried to import low_dim_cython.pyx as:
import numpy
import pyximport
pyximport.install(pyximport.install(setup_args={'include_dirs':[numpy.get_include()]}))
import low_dim_cython
It throws these errors given below.
Traceback (most recent call last):
File "C:\AppData\Local\Continuum\Anaconda3\envs\priview3.4\lib\site-packages\pyximport\pyximport.py", line 216, in load_module
inplace=build_inplace, language_level=language_level)
File "C:\AppData\Local\Continuum\Anaconda3\envs\priview3.4\lib\site-packages\pyximport\pyximport.py", line 192, in build_module
reload_support=pyxargs.reload_support)
File "C:\AppData\Local\Continuum\Anaconda3\envs\priview3.4\lib\site-packages\pyximport\pyxbuild.py", line 102, in pyx_to_dll
dist.run_commands()
File "C:\AppData\Local\Continuum\Anaconda3\envs\priview3.4\lib\distutils\dist.py", line 955, in run_commands
self.run_command(cmd)
File "C:\AppData\Local\Continuum\Anaconda3\envs\priview3.4\lib\distutils\dist.py", line 974, in run_command
cmd_obj.run()
File "C:\AppData\Local\Continuum\Anaconda3\envs\priview3.4\lib\site-packages\Cython\Distutils\old_build_ext.py", line 185, in run
_build_ext.build_ext.run(self)
File "C:\AppData\Local\Continuum\Anaconda3\envs\priview3.4\lib\distutils\command\build_ext.py", line 339, in run
self.build_extensions()
File "C:\AppData\Local\Continuum\Anaconda3\envs\priview3.4\lib\site-packages\Cython\Distutils\old_build_ext.py", line 193, in build_extensions
self.build_extension(ext)
File "C:\AppData\Local\Continuum\Anaconda3\envs\priview3.4\lib\distutils\command\build_ext.py", line 503, in build_extension
depends=ext.depends)
File "C:\AppData\Local\Continuum\Anaconda3\envs\priview3.4\lib\distutils\msvc9compiler.py", line 460, in compile
self.initialize()
File "C:\AppData\Local\Continuum\Anaconda3\envs\priview3.4\lib\distutils\msvc9compiler.py", line 371, in initialize
vc_env = query_vcvarsall(VERSION, plat_spec)
File "C:\AppData\Local\Continuum\Anaconda3\envs\priview3.4\lib\distutils\msvc9compiler.py", line 259, in query_vcvarsall
raise DistutilsPlatformError("Unable to find vcvarsall.bat")
distutils.errors.DistutilsPlatformError: Unable to find vcvarsall.bat
I'm using petrel 0.9.3 and apache storm with the same version. When I try to run a topology I'm getting the following error:
(petrel)[root#localhost example1]# petrel submit --config topology.yaml --logdir `pwd`
[Errno 2] No such file or directory
Traceback (most recent call last):
File "/usr/local/petrel/lib/python2.7/site-packages/petrel-0.9.3.0.3-py2.7.egg/petrel/cmdline.py", line 111, in main
func(**args.__dict__)
File "/usr/local/petrel/lib/python2.7/site-packages/petrel-0.9.3.0.3-py2.7.egg/petrel/cmdline.py", line 32, in submit
sourcejar = get_sourcejar()
File "/usr/local/petrel/lib/python2.7/site-packages/petrel-0.9.3.0.3-py2.7.egg/petrel/cmdline.py", line 23, in get_sourcejar
storm_version = get_storm_version()
File "/usr/local/petrel/lib/python2.7/site-packages/petrel-0.9.3.0.3-py2.7.egg/petrel/cmdline.py", line 17, in get_storm_version
version = subprocess.check_output(['storm', 'version']).strip()
File "/usr/lib64/python2.7/subprocess.py", line 568, in check_output
process = Popen(stdout=PIPE, *popenargs, **kwargs)
File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__
errread, errwrite)
File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child
raise child_exception
I had to add the storm bin location to $PATH