Hello,
I am getting this error towards the end of the command.
galaxy % sh run.sh --no-create-venv --skip-wheels
galaxy % sh run.sh
Activating virtualenv at .venv
Requirement already satisfied: pip>=8.1 in ./.venv/lib/python3.8/site-packages (21.0.1)
Looking in indexes: Package Index, 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
Requirement already satisfied: adal==1.2.4 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 3)) (1.2.4)
Requirement already satisfied: amqp==2.6.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 4)) (2.6.0)
Requirement already satisfied: appdirs==1.4.4 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 5)) (1.4.4)
Requirement already satisfied: attmap==0.12.11 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 6)) (0.12.11)
Requirement already satisfied: attrs==19.3.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 7)) (19.3.0)
Requirement already satisfied: azure-common==1.1.14 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 8)) (1.1.14)
Requirement already satisfied: azure-cosmosdb-nspkg==2.0.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 9)) (2.0.2)
Requirement already satisfied: azure-cosmosdb-table==1.0.4 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 10)) (1.0.4)
Requirement already satisfied: azure-mgmt-compute==4.0.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 11)) (4.0.1)
Requirement already satisfied: azure-mgmt-devtestlabs==2.2.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 12)) (2.2.0)
Requirement already satisfied: azure-mgmt-network==2.1.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 13)) (2.1.0)
Requirement already satisfied: azure-mgmt-nspkg==3.0.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 14)) (3.0.2)
Requirement already satisfied: azure-mgmt-resource==2.0.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 15)) (2.0.0)
Requirement already satisfied: azure-mgmt-storage==2.0.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 16)) (2.0.0)
Requirement already satisfied: azure-nspkg==3.0.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 17)) (3.0.2)
Requirement already satisfied: azure-storage-blob==1.3.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 18)) (1.3.1)
Requirement already satisfied: azure-storage-common==1.4.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 19)) (1.4.2)
Requirement already satisfied: azure-storage-nspkg==3.1.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 20)) (3.1.0)
Requirement already satisfied: babel==2.8.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 21)) (2.8.0)
Requirement already satisfied: bagit==1.7.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 22)) (1.7.0)
Requirement already satisfied: bcrypt==3.1.7 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 23)) (3.1.7)
Requirement already satisfied: bdbag==1.5.6 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 24)) (1.5.6)
Requirement already satisfied: beaker==1.11.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 25)) (1.11.0)
Requirement already satisfied: bioblend==0.13.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 26)) (0.13.0)
Requirement already satisfied: bleach==3.1.5 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 27)) (3.1.5)
Requirement already satisfied: boltons==20.2.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 28)) (20.2.0)
Requirement already satisfied: boto3==1.9.114 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 29)) (1.9.114)
Requirement already satisfied: boto==2.49.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 30)) (2.49.0)
Requirement already satisfied: botocore==1.12.253 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 31)) (1.12.253)
Requirement already satisfied: bx-python==0.8.9 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 32)) (0.8.9)
Requirement already satisfied: cachecontrol==0.11.7 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 33)) (0.11.7)
Requirement already satisfied: cachetools==4.1.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 34)) (4.1.0)
Requirement already satisfied: certifi==2020.6.20 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 35)) (2020.6.20)
Requirement already satisfied: cffi==1.14.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 36)) (1.14.0)
Requirement already satisfied: chardet==3.0.4 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 37)) (3.0.4)
Requirement already satisfied: cheetah3==3.2.5 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 38)) (3.2.5)
Requirement already satisfied: cliff==3.1.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 39)) (3.1.0)
Requirement already satisfied: cloudauthz==0.6.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 40)) (0.6.0)
Requirement already satisfied: cloudbridge==2.0.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 41)) (2.0.0)
Requirement already satisfied: cmd2==0.8.9 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 42)) (0.8.9)
Requirement already satisfied: coloredlogs==14.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 43)) (14.0)
Requirement already satisfied: cryptography==3.2.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 44)) (3.2.1)
Requirement already satisfied: cwltool==1.0.20191225192155 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 45)) (1.0.20191225192155)
Requirement already satisfied: debtcollector==1.22.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 46)) (1.22.0)
Requirement already satisfied: decorator==4.4.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 47)) (4.4.2)
Requirement already satisfied: defusedxml==0.6.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 48)) (0.6.0)
Requirement already satisfied: deprecated==1.2.10 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 49)) (1.2.10)
Requirement already satisfied: deprecation==2.1.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 50)) (2.1.0)
Requirement already satisfied: dictobj==0.4 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 51)) (0.4)
Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 52)) (0.6.2)
Requirement already satisfied: docutils==0.15.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 53)) (0.15.2)
Requirement already satisfied: dogpile.cache==0.9.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 54)) (0.9.2)
Requirement already satisfied: ecdsa==0.15 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 55)) (0.15)
Requirement already satisfied: fabric3==1.14.post1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 56)) (1.14.post1)
Requirement already satisfied: future==0.18.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 57)) (0.18.2)
Requirement already satisfied: futures==3.1.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 58)) (3.1.1)
Requirement already satisfied: galaxy-sequence-utils==1.1.5 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 59)) (1.1.5)
Requirement already satisfied: google-api-python-client==1.7.8 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 60)) (1.7.8)
Requirement already satisfied: google-auth-httplib2==0.0.3 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 61)) (0.0.3)
Requirement already satisfied: google-auth==1.18.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 62)) (1.18.0)
Requirement already satisfied: gxformat2==0.11.3 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 63)) (0.11.3)
Requirement already satisfied: h5py==2.10.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 64)) (2.10.0)
Requirement already satisfied: httplib2==0.18.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 65)) (0.18.1)
Requirement already satisfied: humanfriendly==8.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 66)) (8.2)
Requirement already satisfied: idna==2.9 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 67)) (2.9)
Requirement already satisfied: isa-rwval==0.10.9 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 70)) (0.10.9)
Requirement already satisfied: iso8601==0.1.12 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 71)) (0.1.12)
Requirement already satisfied: isodate==0.6.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 72)) (0.6.0)
Requirement already satisfied: jmespath==0.10.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 73)) (0.10.0)
Requirement already satisfied: jsonpatch==1.26 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 74)) (1.26)
Requirement already satisfied: jsonpointer==2.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 75)) (2.0)
Requirement already satisfied: jsonschema==3.2.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 76)) (3.2.0)
Requirement already satisfied: keystoneauth1==4.1.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 77)) (4.1.0)
Requirement already satisfied: kombu==4.6.11 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 78)) (4.6.11)
Requirement already satisfied: lockfile==0.12.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 79)) (0.12.2)
Requirement already satisfied: lxml==4.6.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 80)) (4.6.2)
Requirement already satisfied: mako==1.1.3 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 81)) (1.1.3)
Requirement already satisfied: markdown==3.2.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 82)) (3.2.2)
Requirement already satisfied: markupsafe==1.1.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 83)) (1.1.1)
Requirement already satisfied: mercurial==5.4.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 84)) (5.4.1)
Requirement already satisfied: mistune==0.8.4 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 85)) (0.8.4)
Requirement already satisfied: msgpack==1.0.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 86)) (1.0.0)
Requirement already satisfied: msrest==0.5.5 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 87)) (0.5.5)
Requirement already satisfied: msrestazure==0.5.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 88)) (0.5.0)
Requirement already satisfied: munch==2.5.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 89)) (2.5.0)
Requirement already satisfied: mypy-extensions==0.4.3 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 90)) (0.4.3)
Requirement already satisfied: netaddr==0.7.20 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 91)) (0.7.20)
Requirement already satisfied: netifaces==0.10.9 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 92)) (0.10.9)
Requirement already satisfied: networkx==1.11 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 93)) (1.11)
Requirement already satisfied: nodeenv==1.4.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 94)) (1.4.0)
Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 95)) (1.3.7)
Requirement already satisfied: numpy==1.18.5 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 96)) (1.18.5)
Requirement already satisfied: oauth2client==4.1.3 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 97)) (4.1.3)
Requirement already satisfied: oauthlib==3.1.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 98)) (3.1.0)
Requirement already satisfied: openstacksdk==0.17.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 99)) (0.17.0)
Requirement already satisfied: os-client-config==2.1.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 100)) (2.1.0)
Requirement already satisfied: os-service-types==1.7.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 101)) (1.7.0)
Requirement already satisfied: osc-lib==2.0.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 102)) (2.0.0)
Requirement already satisfied: oslo.config==7.0.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 103)) (7.0.0)
Requirement already satisfied: oslo.context==2.23.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 104)) (2.23.1)
Requirement already satisfied: oslo.i18n==3.25.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 105)) (3.25.1)
Requirement already satisfied: oslo.log==3.45.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 106)) (3.45.2)
Requirement already satisfied: oslo.serialization==2.29.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 107)) (2.29.2)
Requirement already satisfied: oslo.utils==3.42.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 108)) (3.42.1)
Requirement already satisfied: oyaml==0.9 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 109)) (0.9)
Requirement already satisfied: packaging==20.4 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 110)) (20.4)
Requirement already satisfied: paramiko==2.7.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 111)) (2.7.1)
Requirement already satisfied: parsley==1.3 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 112)) (1.3)
Requirement already satisfied: paste==3.4.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 113)) (3.4.1)
Requirement already satisfied: pastedeploy==2.1.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 114)) (2.1.0)
Requirement already satisfied: pastescript==3.2.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 115)) (3.2.0)
Requirement already satisfied: pbr==5.4.5 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 117)) (5.4.5)
Requirement already satisfied: prettytable==0.7.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 118)) (0.7.2)
Requirement already satisfied: prov==1.5.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 119)) (1.5.1)
Requirement already satisfied: psutil==5.7.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 120)) (5.7.0)
Requirement already satisfied: pulsar-galaxy-lib==0.14.0.dev4 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 121)) (0.14.0.dev4)
Requirement already satisfied: pyasn1-modules==0.2.8 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 122)) (0.2.8)
Requirement already satisfied: pyasn1==0.4.8 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 123)) (0.4.8)
Requirement already satisfied: pycparser==2.20 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 124)) (2.20)
Requirement already satisfied: pycryptodome==3.9.7 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 125)) (3.9.7)
Requirement already satisfied: pyeventsystem==0.1.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 126)) (0.1.0)
Requirement already satisfied: pyjwt==1.7.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 128)) (1.7.1)
Requirement already satisfied: pykwalify==1.7.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 129)) (1.7.0)
Requirement already satisfied: pynacl==1.4.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 130)) (1.4.0)
Requirement already satisfied: pyopenssl==19.1.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 131)) (19.1.0)
Requirement already satisfied: pyparsing==2.4.7 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 132)) (2.4.7)
Requirement already satisfied: pyperclip==1.8.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 133)) (1.8.0)
Requirement already satisfied: pyrsistent==0.16.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 134)) (0.16.0)
Requirement already satisfied: pysam==0.16.0.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 135)) (0.16.0.1)
Requirement already satisfied: pysftp==0.2.9 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 136)) (0.2.9)
Requirement already satisfied: python-cinderclient==4.0.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 137)) (4.0.0)
Requirement already satisfied: python-dateutil==2.8.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 138)) (2.8.1)
Requirement already satisfied: python-glanceclient==2.12.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 139)) (2.12.0)
Requirement already satisfied: python-jose==3.1.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 140)) (3.1.0)
Requirement already satisfied: python-keystoneclient==3.17.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 141)) (3.17.0)
Requirement already satisfied: python-neutronclient==6.9.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 142)) (6.9.0)
Requirement already satisfied: python-novaclient==11.0.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 143)) (11.0.0)
Requirement already satisfied: python-swiftclient==3.6.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 144)) (3.6.0)
Requirement already satisfied: python3-openid==3.1.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 145)) (3.1.0)
Requirement already satisfied: pytz==2020.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 146)) (2020.1)
Requirement already satisfied: pyuwsgi==2.0.19.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 147)) (2.0.19.1)
Requirement already satisfied: pyyaml==5.3.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 148)) (5.3.1)
Requirement already satisfied: rdflib-jsonld==0.4.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 149)) (0.4.0)
Requirement already satisfied: rdflib==4.2.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 150)) (4.2.2)
Requirement already satisfied: refgenconf==0.7.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 151)) (0.7.0)
Requirement already satisfied: repoze.lru==0.7 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 152)) (0.7)
Requirement already satisfied: requests-oauthlib==1.3.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 153)) (1.3.0)
Requirement already satisfied: requests-toolbelt==0.9.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 154)) (0.9.1)
Requirement already satisfied: requests==2.24.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 155)) (2.24.0)
Requirement already satisfied: requestsexceptions==1.4.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 156)) (1.4.0)
Requirement already satisfied: rfc3986==1.4.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 157)) (1.4.0)
Requirement already satisfied: routes==2.4.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 158)) (2.4.1)
Requirement already satisfied: rsa==4.6 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 159)) (4.6)
Requirement already satisfied: ruamel.yaml==0.16.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 161)) (0.16.0)
Requirement already satisfied: s3transfer==0.2.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 162)) (0.2.1)
Requirement already satisfied: scandir==1.10.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 163)) (1.10.0)
Requirement already satisfied: schema-salad==4.5.20191229160203 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 164)) (4.5.20191229160203)
Requirement already satisfied: setuptools-scm==4.1.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 165)) (4.1.2)
Requirement already satisfied: shellescape==3.4.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 166)) (3.4.1)
Requirement already satisfied: simplejson==3.17.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 167)) (3.17.0)
Requirement already satisfied: six==1.15.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 168)) (1.15.0)
Requirement already satisfied: social-auth-core[openidconnect]==3.3.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 169)) (3.3.0)
Requirement already satisfied: sortedcontainers==2.2.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 170)) (2.2.2)
Requirement already satisfied: sqlalchemy-migrate==0.13.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 171)) (0.13.0)
Requirement already satisfied: sqlalchemy-utils==0.36.6 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 172)) (0.36.6)
Requirement already satisfied: sqlalchemy==1.3.17 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 173)) (1.3.17)
Requirement already satisfied: sqlitedict==1.7.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 174)) (1.7.0)
Requirement already satisfied: sqlparse==0.3.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 175)) (0.3.1)
Requirement already satisfied: stevedore==1.32.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 176)) (1.32.0)
Requirement already satisfied: svgwrite==1.3.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 177)) (1.3.1)
Requirement already satisfied: tempita==0.5.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 178)) (0.5.2)
Requirement already satisfied: tenacity==4.12.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 179)) (4.12.0)
Requirement already satisfied: tqdm==4.46.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 180)) (4.46.1)
Requirement already satisfied: typing-extensions==3.7.4.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 181)) (3.7.4.2)
Requirement already satisfied: tzlocal==2.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 183)) (2.1)
Requirement already satisfied: ubiquerg==0.5.2 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 184)) (0.5.2)
Requirement already satisfied: unidecode==1.1.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 185)) (1.1.1)
Requirement already satisfied: uritemplate==3.0.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 186)) (3.0.1)
Requirement already satisfied: urllib3==1.25.9 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 187)) (1.25.9)
Requirement already satisfied: vine==1.3.0 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 188)) (1.3.0)
Requirement already satisfied: warlock==1.3.3 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 189)) (1.3.3)
Requirement already satisfied: wcwidth==0.2.5 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 190)) (0.2.5)
Requirement already satisfied: webencodings==0.5.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 191)) (0.5.1)
Requirement already satisfied: webob==1.8.6 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 192)) (1.8.6)
Requirement already satisfied: whoosh==2.7.4 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 193)) (2.7.4)
Requirement already satisfied: wrapt==1.12.1 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 194)) (1.12.1)
Requirement already satisfied: yacman==0.6.7 in ./.venv/lib/python3.8/site-packages (from -r requirements.txt (line 195)) (0.6.7)
Requirement already satisfied: pathlib2!=2.3.1 in ./.venv/lib/python3.8/site-packages (from cwltool==1.0.20191225192155->-r requirements.txt (line 45)) (2.3.5)
Requirement already satisfied: setuptools in ./.venv/lib/python3.8/site-packages (from cwltool==1.0.20191225192155->-r requirements.txt (line 45)) (52.0.0)
The Galaxy client build is up to date and will not be rebuilt at this time.
Activating virtualenv at .venv
Traceback (most recent call last):
File “/Users/shahid/galaxy/lib/galaxy/util/filelock.py”, line 43, in acquire
self.fd = os.open(self.lockfile, os.O_CREAT | os.O_EXCL | os.O_RDWR)
FileExistsError: [Errno 17] File exists: ‘/Users/shahid/galaxy/database/dependencies/conda.lock’
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/Users/shahid/galaxy/lib/galaxy/tool_util/deps/installable.py”, line 70, in ensure_installed
with FileLock(os.path.join(parent_path, desc.lower()), timeout=300):
File “/Users/shahid/galaxy/lib/galaxy/util/filelock.py”, line 68, in enter
self.acquire()
File “/Users/shahid/galaxy/lib/galaxy/util/filelock.py”, line 49, in acquire
raise FileLockException(“Timeout occurred.”)
galaxy.util.filelock.FileLockException: Timeout occurred.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “./scripts/manage_tool_dependencies.py”, line 40, in
main()
File “/Users/shahid/galaxy/lib/galaxy/util/script.py”, line 45, in main
action_func(args, kwargs)
File “./scripts/manage_tool_dependencies.py”, line 16, in _init_if_needed
_build_dependency_manager_no_config(kwargs)
File “./scripts/manage_tool_dependencies.py”, line 29, in _build_dependency_manager_no_config
dependency_manager = build_dependency_manager(app_config_dict=kwargs, conf_file=dependency_resolvers_config_file, default_tool_dependency_dir=“database/dependencies”)
File “/Users/shahid/galaxy/lib/galaxy/tool_util/deps/init.py”, line 90, in build_dependency_manager
dependency_manager = DependencyManager(**dependency_manager_kwds)
File “/Users/shahid/galaxy/lib/galaxy/tool_util/deps/init.py”, line 131, in init
self.dependency_resolvers = self.__parse_resolver_conf_plugins(plugin_source)
File “/Users/shahid/galaxy/lib/galaxy/tool_util/deps/init.py”, line 333, in __parse_resolver_conf_plugins
return plugin_config.load_plugins(self.resolver_classes, plugin_source, extra_kwds, plugin_type_keys=[‘type’, ‘resolver_type’])
File “/Users/shahid/galaxy/lib/galaxy/util/plugin_config.py”, line 37, in load_plugins
return __load_plugins_from_dicts(plugins_dict, plugin_source.source, extra_kwds, plugin_type_keys=plugin_type_keys)
File “/Users/shahid/galaxy/lib/galaxy/util/plugin_config.py”, line 81, in __load_plugins_from_dicts
plugin = plugins_dictplugin_type
File “/Users/shahid/galaxy/lib/galaxy/tool_util/deps/resolvers/conda.py”, line 138, in init
self.disabled = not galaxy.tool_util.deps.installable.ensure_installed(conda_context, install_conda, self.auto_init)
File “/Users/shahid/galaxy/lib/galaxy/tool_util/deps/installable.py”, line 75, in ensure_installed
raise Exception(“Failed to get file lock for %s” % os.path.join(parent_path, desc.lower()))
Exception: Failed to get file lock for /Users/shahid/galaxy/database/dependencies/conda
Executing: .venv/bin/uwsgi --module ‘galaxy.webapps.galaxy.buildapp:uwsgi_app()’ --virtualenv /Users/shahid/galaxy/.venv --static-safe /Users/shahid/galaxy/client/src/assets --pythonpath lib --threads 4 --buffer-size 16384 --http localhost:8080 --static-map /static=/Users/shahid/galaxy/static --static-map /favicon.ico=/Users/shahid/galaxy/static/favicon.ico --die-on-term --hook-master-start ‘unix_signal:2 gracefully_kill_them_all’ --hook-master-start ‘unix_signal:15 gracefully_kill_them_all’ --enable-threads --umask 027 --py-call-osafterfork
dyld: Library not loaded: @rpath/libpcre.1.dylib
Referenced from: /Users/shahid/galaxy/.venv/bin/uwsgi
Reason: image not found
run.sh: line 91: 20602 Abort trap: 6 .venv/bin/uwsgi --module ‘galaxy.webapps.galaxy.buildapp:uwsgi_app()’ --virtualenv /Users/shahid/galaxy/.venv --static-safe /Users/shahid/galaxy/client/src/assets --pythonpath lib --threads 4 --buffer-size 16384 --http localhost:8080 --static-map /static=/Users/shahid/galaxy/static --static-map /favicon.ico=/Users/shahid/galaxy/static/favicon.ico --die-on-term --hook-master-start ‘unix_signal:2 gracefully_kill_them_all’ --hook-master-start ‘unix_signal:15 gracefully_kill_them_all’ --enable-threads --umask 027 --py-call-osafterfork
(base) shahid@Shahids-MacBook-Pro galaxy %