Trouble installing ipyrad

[YaraAlshw]

I followed the steps in this tutorial: https://radcamp.github.io/Yale2019/ipyrad_Install_Quickstart.html to install ipyrad on Grace. Everything seemed to work fine, as I continued with the tutorial part 1 and tried the "help" command, I got the following errors:

(ipyrad)[eeb354_yaa23@ondemand1 project]$ ipyrad --help

Traceback (most recent call last): File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/bin/ipyrad", line 6, in from pkg_resources import load_entry_point File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/pkg_resources/init.py", line 3267, in @_call_aside File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/pkg_resources/init.py", line 3251, in _call_aside f(*args, *kwargs) File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/pkg_resources/init.py", line 3280, in _initialize_master_wo rking_set working_set = WorkingSet._build_master() File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/pkg_resources/init.py", line 582, in _build_master ws.require(requires) File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/pkg_resources/init.py", line 899, in require needed = self.resolve(parse_requirements(requirements)) File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/pkg_resources/init.py", line 785, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'ipyrad==0.7.17' distribution was not found and is required by the application (ipyrad)[eeb354_yaa23@ondemand1 project]$ ipyrad --help Traceback (most recent call last): File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/bin/ipyrad", line 6, in from pkg_resources import load_entry_point File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/pkg_resources/init.py", line 3267, in @_call_aside File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/pkg_resources/init.py", line 3251, in _call_aside f(args, **kwargs) File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/pkg_resources/init.py", line 3280, in _initialize_master_wo rking_set working_set = WorkingSet._build_master() File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/pkg_resources/init.py", line 582, in _build_master ws.require(requires) File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/pkg_resources/init.py", line 899, in require needed = self.resolve(parse_requirements(requirements)) File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/pkg_resources/init.py", line 785, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'ipyrad==0.7.17' distribution was not found and is required by the application

[YaraAlshw]

Trying this again gave this error:

"(ipyrad)[eeb354_yaa23@ondemand1 project]$ ipyrad --help Traceback (most recent call last): File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/bin/ipyrad", line 33, in sys.exit(load_entry_point('ipyrad==0.1.32', 'console_scripts', 'ipyrad')()) File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/bin/ipyrad", line 25, in importlib_load_e ntry_point return next(matches).load() File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/importlib_met adata/init.py", line 105, in load module = import_module(match.group('module')) File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/importlib/init.py", lin e 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 994, in _gcd_import File "", line 971, in _find_and_load File "", line 941, in _find_and_load_unlocked File "", line 219, in _call_with_frames_removed File "", line 994, in _gcd_import File "", line 971, in _find_and_load File "", line 955, in _find_and_load_unlocked File "", line 665, in _load_unlocked File "", line 678, in exec_module File "", line 219, in _call_with_frames_removed File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32 -py3.6.egg/ipyrad/init.py", line 4, in from . import load File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32 -py3.6.egg/ipyrad/load/init.py", line 16, in from .load import load_assembly File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32 -py3.6.egg/ipyrad/load/load.py", line 13, in from ipyrad.core.assembly import Assembly File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32 -py3.6.egg/ipyrad/core/assembly.py", line 27, in from ipyrad.assemble.util import File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32 -py3.6.egg/ipyrad/assemble/init.py", line 2, in from . import demultiplex File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32-py3.6.egg/ipyrad/assemble/demultiplex.py", line 14, in import cPickle as pickle ModuleNotFoundError: No module named 'cPickle' (ipyrad)[eeb354_yaa23@ondemand1 project]$ --help bash: --help: command not found... (ipyrad)[eeb354_yaa23@ondemand1 project]$ conda --version conda 4.8.3 (ipyrad)[eeb354_yaa23@ondemand1 project]$ ipyrad --version Traceback (most recent call last): File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/bin/ipyrad", line 33, in sys.exit(load_entry_point('ipyrad==0.1.32', 'console_scripts', 'ipyrad')()) File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/bin/ipyrad", line 25, in importlib_load_entry_point return next(matches).load() File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/importlib_metadata/init.py", line 105, in load module = import_module(match.group('module')) File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/importlib/init.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 994, in _gcd_import File "", line 971, in _find_and_load File "", line 941, in _find_and_load_unlocked File "", line 219, in _call_with_frames_removed File "", line 994, in _gcd_import File "", line 971, in _find_and_load File "", line 955, in _find_and_load_unlocked File "", line 665, in _load_unlocked File "", line 678, in exec_module File "", line 219, in _call_with_frames_removed File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32-py3.6.egg/ipyrad/init.py", line 4, in from . import load File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32-py3.6.egg/ipyrad/load/init.py", line 16, in from .load import load_assembly File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32-py3.6.egg/ipyrad/load/load.py", line 13, in from ipyrad.core.assembly import Assembly File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32-py3.6.egg/ipyrad/core/assembly.py", line 27, in from ipyrad.assemble.util import File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32-py3.6.egg/ipyrad/assemble/init.py", line 2, in from . import demultiplex File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32-py3.6.egg/ipyrad/assemble/demultiplex.py", line 14, in import cPickle as pickle ModuleNotFoundError: No module named 'cPickle' (ipyrad)[eeb354_yaa23@ondemand1 project]$ source activate ipyrad (ipyrad)[eeb354_yaa23@ondemand1 project]$ ipyrad --help Traceback (most recent call last): File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/bin/ipyrad", line 33, in sys.exit(load_entry_point('ipyrad==0.1.32', 'console_scripts', 'ipyrad')()) File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/bin/ipyrad", line 25, in importlib_load_entry_point return next(matches).load() File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/importlib_metadata/init.py", line 105, in load module = import_module(match.group('module')) File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/importlib/init.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 994, in _gcd_import File "", line 971, in _find_and_load File "", line 941, in _find_and_load_unlocked File "", line 219, in _call_with_frames_removed File "", line 994, in _gcd_import File "", line 971, in _find_and_load File "", line 955, in _find_and_load_unlocked File "", line 665, in _load_unlocked File "", line 678, in exec_module File "", line 219, in _call_with_frames_removed File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32-py3.6.egg/ipyrad/init.py", line 4, in from . import load File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32-py3.6.egg/ipyrad/load/init.py", line 16, in from .load import load_assembly File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32-py3.6.egg/ipyrad/load/load.py", line 13, in from ipyrad.core.assembly import Assembly File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32-py3.6.egg/ipyrad/core/assembly.py", line 27, in from ipyrad.assemble.util import File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32-py3.6.egg/ipyrad/assemble/init.py", line 2, in from . import demultiplex File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32-py3.6.egg/ipyrad/assemble/demultiplex.py", line 14, in import cPickle as pickle ModuleNotFoundError: No module named 'cPickle' (ipyrad)[eeb354_yaa23@ondemand1 project]$ ipyrad -n test1 Traceback (most recent call last): File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/bin/ipyrad", line 33, in sys.exit(load_entry_point('ipyrad==0.1.32', 'console_scripts', 'ipyrad')()) File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/bin/ipyrad", line 25, in importlib_load_entry_point return next(matches).load() File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/importlib_metadata/init.py", line 105, in load module = import_module(match.group('module')) File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/importlib/init.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 994, in _gcd_import File "", line 971, in _find_and_load File "", line 941, in _find_and_load_unlocked File "", line 219, in _call_with_frames_removed File "", line 994, in _gcd_import File "", line 971, in _find_and_load File "", line 955, in _find_and_load_unlocked File "", line 665, in _load_unlocked File "", line 678, in exec_module File "", line 219, in _call_with_frames_removed File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32-py3.6.egg/ipyrad/init.py", line 4, in from . import load File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32-py3.6.egg/ipyrad/load/init.py", line 16, in from .load import load_assembly File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32-py3.6.egg/ipyrad/load/load.py", line 13, in from ipyrad.core.assembly import Assembly File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32-py3.6.egg/ipyrad/core/assembly.py", line 27, in from ipyrad.assemble.util import File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32-py3.6.egg/ipyrad/assemble/init.py", line 2, in from . import demultiplex File "/gpfs/loomis/project/eeb354/eeb354_yaa23/conda_envs/ipyrad/lib/python3.6/site-packages/ipyrad-0.1.32-py3.6.egg/ipyrad/assemble/demultiplex.py", line 14, in import cPickle as pickle ModuleNotFoundError: No module named 'cPickle'"

[YaraAlshw]

Fixed the issue with the following commands to create an ipyrad environment in a different way (thanks to Lauren and Ben!)

module load miniconda conda create -n ipyrad ipyrad notebook

[caseywdunn]

Very glad to hear that this works.