Hi,
I am new to using terminal and Usegalaxy - I have run all the steps for installation, but seem to be running into an error after the sh run.sh command. I have ensured Cython is installed. Please could someone look at the error below and assist. Thank you.
(.venv) izaakha@Izaaks-MacBook-Pro galaxy % sh run.sh
Activating virtualenv at .venv
Requirement already satisfied: pip>=8.1 in ./.venv/lib/python3.11/site-packages (23.2.1)
Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple
Ignoring importlib-metadata: markers 'python_version < "3.8"' don't match your environment
Ignoring importlib-resources: markers 'python_version < "3.7"' don't match your environment
Ignoring pathlib2: markers 'python_version < "3.6"' don't match your environment
Ignoring pyinotify: markers 'sys_platform != "win32" and sys_platform != "darwin" and sys_platform != "sunos5"' don't match your environment
Ignoring ruamel.yaml.clib: markers 'platform_python_implementation == "CPython" and python_version < "3.8"' don't match your environment
Ignoring typing: markers 'python_version < "3.5"' don't match your environment
Ignoring zipp: markers 'python_version < "3.8"' don't match your environment
Collecting adal==1.2.4 (from -r requirements.txt (line 3))
Using cached adal-1.2.4-py2.py3-none-any.whl (55 kB)
Collecting amqp==2.6.0 (from -r requirements.txt (line 4))
Using cached amqp-2.6.0-py2.py3-none-any.whl (47 kB)
Collecting appdirs==1.4.4 (from -r requirements.txt (line 5))
Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
Collecting attmap==0.12.11 (from -r requirements.txt (line 6))
Using cached https://wheels.galaxyproject.org/simple/attmap/attmap-0.12.11-py3-none-any.whl (12 kB)
Collecting attrs==19.3.0 (from -r requirements.txt (line 7))
Using cached attrs-19.3.0-py2.py3-none-any.whl (39 kB)
Collecting azure-common==1.1.14 (from -r requirements.txt (line 8))
Using cached azure_common-1.1.14-py2.py3-none-any.whl (10 kB)
Collecting azure-cosmosdb-nspkg==2.0.2 (from -r requirements.txt (line 9))
Using cached azure_cosmosdb_nspkg-2.0.2-py2.py3-none-any.whl (2.9 kB)
Collecting azure-cosmosdb-table==1.0.4 (from -r requirements.txt (line 10))
Using cached azure_cosmosdb_table-1.0.4-py2.py3-none-any.whl (82 kB)
Collecting azure-mgmt-compute==4.0.1 (from -r requirements.txt (line 11))
Using cached azure_mgmt_compute-4.0.1-py2.py3-none-any.whl (2.1 MB)
Collecting azure-mgmt-devtestlabs==2.2.0 (from -r requirements.txt (line 12))
Using cached azure_mgmt_devtestlabs-2.2.0-py2.py3-none-any.whl (194 kB)
Collecting azure-mgmt-network==2.1.0 (from -r requirements.txt (line 13))
Using cached azure_mgmt_network-2.1.0-py2.py3-none-any.whl (6.9 MB)
Collecting azure-mgmt-nspkg==3.0.2 (from -r requirements.txt (line 14))
Using cached azure_mgmt_nspkg-3.0.2-py3-none-any.whl (1.6 kB)
Collecting azure-mgmt-resource==2.0.0 (from -r requirements.txt (line 15))
Using cached azure_mgmt_resource-2.0.0-py2.py3-none-any.whl (698 kB)
Collecting azure-mgmt-storage==2.0.0 (from -r requirements.txt (line 16))
Using cached azure_mgmt_storage-2.0.0-py2.py3-none-any.whl (558 kB)
Collecting azure-nspkg==3.0.2 (from -r requirements.txt (line 17))
Using cached azure_nspkg-3.0.2-py3-none-any.whl (1.5 kB)
Collecting azure-storage-blob==1.3.1 (from -r requirements.txt (line 18))
Using cached azure_storage_blob-1.3.1-py2.py3-none-any.whl (77 kB)
Collecting azure-storage-common==1.4.2 (from -r requirements.txt (line 19))
Using cached azure_storage_common-1.4.2-py2.py3-none-any.whl (47 kB)
Collecting azure-storage-nspkg==3.1.0 (from -r requirements.txt (line 20))
Using cached azure_storage_nspkg-3.1.0-py2.py3-none-any.whl (1.7 kB)
Collecting babel==2.8.0 (from -r requirements.txt (line 21))
Using cached Babel-2.8.0-py2.py3-none-any.whl (8.6 MB)
Collecting bagit==1.7.0 (from -r requirements.txt (line 22))
Using cached https://wheels.galaxyproject.org/simple/bagit/bagit-1.7.0-py2.py3-none-any.whl (34 kB)
Collecting bcrypt==3.1.7 (from -r requirements.txt (line 23))
Using cached bcrypt-3.1.7.tar.gz (42 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting bdbag==1.5.6 (from -r requirements.txt (line 24))
Using cached bdbag-1.5.6-py2.py3-none-any.whl (66 kB)
Collecting beaker==1.11.0 (from -r requirements.txt (line 25))
Using cached Beaker-1.11.0.tar.gz (40 kB)
Preparing metadata (setup.py) ... done
Collecting bioblend==0.13.0 (from -r requirements.txt (line 26))
Using cached bioblend-0.13.0-py2.py3-none-any.whl (125 kB)
Collecting bleach==3.1.5 (from -r requirements.txt (line 27))
Using cached bleach-3.1.5-py2.py3-none-any.whl (151 kB)
Collecting boltons==20.2.0 (from -r requirements.txt (line 28))
Using cached boltons-20.2.0-py2.py3-none-any.whl (171 kB)
Collecting boto3==1.9.114 (from -r requirements.txt (line 29))
Using cached boto3-1.9.114-py2.py3-none-any.whl (128 kB)
Collecting boto==2.49.0 (from -r requirements.txt (line 30))
Using cached boto-2.49.0-py2.py3-none-any.whl (1.4 MB)
Collecting botocore==1.12.253 (from -r requirements.txt (line 31))
Using cached botocore-1.12.253-py2.py3-none-any.whl (5.7 MB)
Collecting bx-python==0.8.9 (from -r requirements.txt (line 32))
Using cached bx-python-0.8.9.tar.gz (1.4 MB)
Preparing metadata (setup.py) ... done
Collecting cachecontrol==0.11.7 (from -r requirements.txt (line 33))
Using cached CacheControl-0.11.7.tar.gz (13 kB)
Preparing metadata (setup.py) ... done
Collecting cachetools==4.1.0 (from -r requirements.txt (line 34))
Using cached cachetools-4.1.0-py3-none-any.whl (10 kB)
Collecting certifi==2020.6.20 (from -r requirements.txt (line 35))
Using cached certifi-2020.6.20-py2.py3-none-any.whl (156 kB)
Collecting cffi==1.14.0 (from -r requirements.txt (line 36))
Using cached cffi-1.14.0.tar.gz (463 kB)
Preparing metadata (setup.py) ... done
Collecting chardet==3.0.4 (from -r requirements.txt (line 37))
Using cached chardet-3.0.4-py2.py3-none-any.whl (133 kB)
Collecting cheetah3==3.2.5 (from -r requirements.txt (line 38))
Using cached Cheetah3-3.2.5.tar.gz (295 kB)
Preparing metadata (setup.py) ... done
Collecting cliff==3.1.0 (from -r requirements.txt (line 39))
Using cached cliff-3.1.0-py3-none-any.whl (80 kB)
Collecting cloudauthz==0.6.0 (from -r requirements.txt (line 40))
Using cached cloudauthz-0.6.0-py2.py3-none-any.whl (8.9 kB)
Collecting cloudbridge==2.0.0 (from -r requirements.txt (line 41))
Using cached cloudbridge-2.0.0-py2.py3-none-any.whl (182 kB)
Collecting cmd2==0.8.9 (from -r requirements.txt (line 42))
Using cached cmd2-0.8.9-py2.py3-none-any.whl (53 kB)
Collecting coloredlogs==14.0 (from -r requirements.txt (line 43))
Using cached coloredlogs-14.0-py2.py3-none-any.whl (43 kB)
Collecting cryptography==3.2.1 (from -r requirements.txt (line 44))
Using cached cryptography-3.2.1.tar.gz (540 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting cwltool==1.0.20191225192155 (from -r requirements.txt (line 45))
Using cached cwltool-1.0.20191225192155-py2.py3-none-any.whl (725 kB)
Collecting debtcollector==1.22.0 (from -r requirements.txt (line 46))
Using cached debtcollector-1.22.0-py2.py3-none-any.whl (23 kB)
Collecting decorator==4.4.2 (from -r requirements.txt (line 47))
Using cached decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)
Collecting defusedxml==0.6.0 (from -r requirements.txt (line 48))
Using cached defusedxml-0.6.0-py2.py3-none-any.whl (23 kB)
Collecting deprecated==1.2.10 (from -r requirements.txt (line 49))
Using cached Deprecated-1.2.10-py2.py3-none-any.whl (8.7 kB)
Collecting deprecation==2.1.0 (from -r requirements.txt (line 50))
Using cached deprecation-2.1.0-py2.py3-none-any.whl (11 kB)
Collecting dictobj==0.4 (from -r requirements.txt (line 51))
Using cached dictobj-0.4.tar.gz (6.9 kB)
Preparing metadata (setup.py) ... done
Collecting docopt==0.6.2 (from -r requirements.txt (line 52))
Using cached https://wheels.galaxyproject.org/simple/docopt/docopt-0.6.2-py2.py3-none-any.whl (19 kB)
Collecting docutils==0.15.2 (from -r requirements.txt (line 53))
Using cached docutils-0.15.2-py3-none-any.whl (547 kB)
Collecting dogpile.cache==0.9.2 (from -r requirements.txt (line 54))
Using cached dogpile.cache-0.9.2.tar.gz (329 kB)
Preparing metadata (setup.py) ... done
Collecting ecdsa==0.15 (from -r requirements.txt (line 55))
Using cached ecdsa-0.15-py2.py3-none-any.whl (100 kB)
Collecting fabric3==1.14.post1 (from -r requirements.txt (line 56))
Using cached Fabric3-1.14.post1-py3-none-any.whl (92 kB)
Collecting future==0.18.2 (from -r requirements.txt (line 57))
Using cached future-0.18.2.tar.gz (829 kB)
Preparing metadata (setup.py) ... done
Collecting futures==3.1.1 (from -r requirements.txt (line 58))
Using cached https://wheels.galaxyproject.org/simple/futures/futures-3.1.1.tar.gz (26 kB)
Preparing metadata (setup.py) ... done
Collecting galaxy-sequence-utils==1.1.5 (from -r requirements.txt (line 59))
Using cached galaxy_sequence_utils-1.1.5-py2.py3-none-any.whl (37 kB)
Collecting google-api-python-client==1.7.8 (from -r requirements.txt (line 60))
Using cached google_api_python_client-1.7.8-py3-none-any.whl (56 kB)
Collecting google-auth-httplib2==0.0.3 (from -r requirements.txt (line 61))
Using cached google_auth_httplib2-0.0.3-py2.py3-none-any.whl (6.3 kB)
Collecting google-auth==1.18.0 (from -r requirements.txt (line 62))
Using cached google_auth-1.18.0-py2.py3-none-any.whl (90 kB)
Collecting gxformat2==0.11.3 (from -r requirements.txt (line 63))
Using cached gxformat2-0.11.3-py2.py3-none-any.whl (40 kB)
Collecting h5py==2.10.0 (from -r requirements.txt (line 64))
Using cached h5py-2.10.0.tar.gz (301 kB)
Preparing metadata (setup.py) ... done
Collecting httplib2==0.18.1 (from -r requirements.txt (line 65))
Using cached httplib2-0.18.1-py3-none-any.whl (95 kB)
Collecting humanfriendly==8.2 (from -r requirements.txt (line 66))
Using cached humanfriendly-8.2-py2.py3-none-any.whl (86 kB)
Collecting idna==2.9 (from -r requirements.txt (line 67))
Using cached idna-2.9-py2.py3-none-any.whl (58 kB)
Collecting isa-rwval==0.10.9 (from -r requirements.txt (line 70))
Using cached isa_rwval-0.10.9-py2.py3-none-any.whl (40 kB)
Collecting iso8601==0.1.12 (from -r requirements.txt (line 71))
Using cached iso8601-0.1.12-py3-none-any.whl (12 kB)
Collecting isodate==0.6.0 (from -r requirements.txt (line 72))
Using cached isodate-0.6.0-py2.py3-none-any.whl (45 kB)
Collecting jmespath==0.10.0 (from -r requirements.txt (line 73))
Using cached jmespath-0.10.0-py2.py3-none-any.whl (24 kB)
Collecting jsonpatch==1.26 (from -r requirements.txt (line 74))
Using cached jsonpatch-1.26-py2.py3-none-any.whl (11 kB)
Collecting jsonpointer==2.0 (from -r requirements.txt (line 75))
Using cached jsonpointer-2.0-py2.py3-none-any.whl (7.6 kB)
Collecting jsonschema==3.2.0 (from -r requirements.txt (line 76))
Using cached jsonschema-3.2.0-py2.py3-none-any.whl (56 kB)
Collecting keystoneauth1==4.1.0 (from -r requirements.txt (line 77))
Using cached keystoneauth1-4.1.0-py3-none-any.whl (305 kB)
Collecting kombu==4.6.11 (from -r requirements.txt (line 78))
Using cached kombu-4.6.11-py2.py3-none-any.whl (184 kB)
Collecting lockfile==0.12.2 (from -r requirements.txt (line 79))
Using cached lockfile-0.12.2-py2.py3-none-any.whl (13 kB)
Collecting lxml==4.6.2 (from -r requirements.txt (line 80))
Using cached lxml-4.6.2.tar.gz (3.2 MB)
Preparing metadata (setup.py) ... done
Collecting mako==1.1.3 (from -r requirements.txt (line 81))
Using cached Mako-1.1.3-py2.py3-none-any.whl (75 kB)
Collecting markdown==3.2.2 (from -r requirements.txt (line 82))
Using cached Markdown-3.2.2-py3-none-any.whl (88 kB)
Collecting markupsafe==1.1.1 (from -r requirements.txt (line 83))
Using cached MarkupSafe-1.1.1.tar.gz (19 kB)
Preparing metadata (setup.py) ... done
Collecting mercurial==5.4.1 (from -r requirements.txt (line 84))
Using cached mercurial-5.4.1.tar.gz (7.7 MB)
Preparing metadata (setup.py) ... done
Collecting mistune==0.8.4 (from -r requirements.txt (line 85))
Using cached mistune-0.8.4-py2.py3-none-any.whl (16 kB)
Collecting msgpack==1.0.0 (from -r requirements.txt (line 86))
Using cached msgpack-1.0.0.tar.gz (232 kB)
Preparing metadata (setup.py) ... done
Collecting msrest==0.5.5 (from -r requirements.txt (line 87))
Using cached msrest-0.5.5-py2.py3-none-any.whl (47 kB)
Collecting msrestazure==0.5.0 (from -r requirements.txt (line 88))
Using cached msrestazure-0.5.0-py2.py3-none-any.whl (36 kB)
Collecting munch==2.5.0 (from -r requirements.txt (line 89))
Using cached munch-2.5.0-py2.py3-none-any.whl (10 kB)
Collecting mypy-extensions==0.4.3 (from -r requirements.txt (line 90))
Using cached mypy_extensions-0.4.3-py2.py3-none-any.whl (4.5 kB)
Collecting netaddr==0.7.20 (from -r requirements.txt (line 91))
Using cached netaddr-0.7.20-py2.py3-none-any.whl (1.9 MB)
Collecting netifaces==0.10.9 (from -r requirements.txt (line 92))
Using cached netifaces-0.10.9.tar.gz (28 kB)
Preparing metadata (setup.py) ... done
Collecting networkx==1.11 (from -r requirements.txt (line 93))
Using cached networkx-1.11-py2.py3-none-any.whl (1.3 MB)
Collecting nodeenv==1.4.0 (from -r requirements.txt (line 94))
Using cached nodeenv-1.4.0-py2.py3-none-any.whl (21 kB)
Collecting nose==1.3.7 (from -r requirements.txt (line 95))
Using cached nose-1.3.7-py3-none-any.whl (154 kB)
Collecting numpy==1.18.5 (from -r requirements.txt (line 96))
Using cached numpy-1.18.5.zip (5.4 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... error
error: subprocess-exited-with-error
× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [58 lines of output]
Running from numpy source directory.
<string>:461: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates
/private/var/folders/32/cr0yjsln65z1d1w_9r19qbww0000gn/T/pip-install-sqm1ipow/numpy_d3c5c5ededd5430ebb53dad40e13874f/tools/cythonize.py:75: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
required_version = LooseVersion('0.29.14')
/private/var/folders/32/cr0yjsln65z1d1w_9r19qbww0000gn/T/pip-install-sqm1ipow/numpy_d3c5c5ededd5430ebb53dad40e13874f/tools/cythonize.py:77: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
if LooseVersion(cython_version) < required_version:
warning: _philox.pyx:19:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
warning: /private/var/folders/32/cr0yjsln65z1d1w_9r19qbww0000gn/T/pip-install-sqm1ipow/numpy_d3c5c5ededd5430ebb53dad40e13874f/numpy/__init__.pxd:17:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
Error compiling Cython file:
------------------------------------------------------------
...
self.rng_state.ctr.v[i] = counter[i]
self._reset_state_variables()
self._bitgen.state = <void *>&self.rng_state
self._bitgen.next_uint64 = &philox_uint64
^
------------------------------------------------------------
_philox.pyx:195:35: Cannot assign type 'uint64_t (*)(void *) except? -1 nogil' to 'uint64_t (*)(void *) noexcept nogil'. Exception values are incompatible. Suggest adding 'noexcept' to type 'uint64_t (void *) except? -1 nogil'.
Processing numpy/random/_bounded_integers.pxd.in
Processing numpy/random/_philox.pyx
Traceback (most recent call last):
File "/private/var/folders/32/cr0yjsln65z1d1w_9r19qbww0000gn/T/pip-install-sqm1ipow/numpy_d3c5c5ededd5430ebb53dad40e13874f/tools/cythonize.py", line 238, in <module>
main()
File "/private/var/folders/32/cr0yjsln65z1d1w_9r19qbww0000gn/T/pip-install-sqm1ipow/numpy_d3c5c5ededd5430ebb53dad40e13874f/tools/cythonize.py", line 234, in main
find_process_files(root_dir)
File "/private/var/folders/32/cr0yjsln65z1d1w_9r19qbww0000gn/T/pip-install-sqm1ipow/numpy_d3c5c5ededd5430ebb53dad40e13874f/tools/cythonize.py", line 225, in find_process_files
process(root_dir, fromfile, tofile, function, hash_db)
File "/private/var/folders/32/cr0yjsln65z1d1w_9r19qbww0000gn/T/pip-install-sqm1ipow/numpy_d3c5c5ededd5430ebb53dad40e13874f/tools/cythonize.py", line 191, in process
processor_function(fromfile, tofile)
File "/private/var/folders/32/cr0yjsln65z1d1w_9r19qbww0000gn/T/pip-install-sqm1ipow/numpy_d3c5c5ededd5430ebb53dad40e13874f/tools/cythonize.py", line 80, in process_pyx
subprocess.check_call(
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/Users/izaakha/Desktop/usegalaxy/galaxy/.venv/bin/python', '-m', 'cython', '-3', '--fast-fail', '-o', '_philox.c', '_philox.pyx']' returned non-zero exit status 1.
Cythonizing sources
Traceback (most recent call last):
File "/Users/izaakha/Desktop/usegalaxy/galaxy/.venv/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/Users/izaakha/Desktop/usegalaxy/galaxy/.venv/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/izaakha/Desktop/usegalaxy/galaxy/.venv/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 149, in prepare_metadata_for_build_wheel
return hook(metadata_directory, config_settings)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/private/var/folders/32/cr0yjsln65z1d1w_9r19qbww0000gn/T/pip-build-env-plsl80j8/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 396, in prepare_metadata_for_build_wheel
self.run_setup()
File "/private/var/folders/32/cr0yjsln65z1d1w_9r19qbww0000gn/T/pip-build-env-plsl80j8/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 507, in run_setup
super(_BuildMetaLegacyBackend, self).run_setup(setup_script=setup_script)
File "/private/var/folders/32/cr0yjsln65z1d1w_9r19qbww0000gn/T/pip-build-env-plsl80j8/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 341, in run_setup
exec(code, locals())
File "<string>", line 488, in <module>
File "<string>", line 469, in setup_package
File "<string>", line 275, in generate_cython
RuntimeError: Running cythonize failed!
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.