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mil2041 / netboxr

An R package to mark functional modules in the network analysis using data from pathwayCommons
https://mil2041.github.io/netboxr/
GNU Lesser General Public License v3.0
3 stars 5 forks source link

Issues setting up Galaxy instance #33

Closed sajo25 closed 2 years ago

sajo25 commented 2 years ago

I'm trying to set up a Galaxy instance (instructions) where I will then try to install the netboxr tool from the Tool Shed. I've encountered an issue with the installation and I've included the terminal output below:

~/galaxy$ sh run.sh
Activating virtualenv at .venv
Requirement already satisfied: pip>=19.3 in ./.venv/lib/python3.7/site-packages (22.0.4)
WARNING: You are using pip version 22.0.4; however, version 22.1.2 is available.
You should consider upgrading via the '/home/ubuntu/galaxy/.venv/bin/python -m pip install --upgrade pip' command.
Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple
Ignoring atomicwrites: markers 'python_version >= "3.7" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.7" and python_full_version >= "3.4.0"' don't match your environment
Ignoring colorama: markers 'sys_platform == "win32" and python_version >= "3.7" and python_full_version >= "3.6.2" and platform_system == "Windows" and (python_version >= "2.7" and python_full_version < "3.0.0" and platform_system == "Windows" or python_full_version >= "3.5.0" and platform_system == "Windows") and (python_version >= "3.7" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.7" and python_full_version >= "3.5.0") and (python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") or sys_platform == "win32" and python_version >= "3.6" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") and python_full_version >= "3.5.0")' don't match your environment
Ignoring py: markers 'python_version >= "3.7" and python_full_version < "3.0.0" and implementation_name == "pypy" or python_full_version >= "3.5.0" and python_version >= "3.7" and implementation_name == "pypy"' don't match your environment
Ignoring pyreadline3: markers 'sys_platform == "win32" and python_version >= "3.8" and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0")' don't match your environment
Ignoring pyreadline: markers 'sys_platform == "win32" and python_version < "3.8" and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0")' don't match your environment
Requirement already satisfied: a2wsgi==1.4.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) (1.4.1)
Requirement already satisfied: adal==1.2.7 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) (1.2.7)
Requirement already satisfied: aiofiles==0.8.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 5)) (0.8.0)
Requirement already satisfied: alabaster==0.7.12 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 6)) (0.7.12)
Requirement already satisfied: alembic==1.8.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 7)) (1.8.0)
Requirement already satisfied: amqp==5.1.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 8)) (5.1.1)
Requirement already satisfied: anyio==3.6.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 9)) (3.6.1)
Requirement already satisfied: apispec==5.2.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 10)) (5.2.2)
Requirement already satisfied: appdirs==1.4.4 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 11)) (1.4.4)
Requirement already satisfied: argcomplete==2.0.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 12)) (2.0.0)
Requirement already satisfied: ase==3.22.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 13)) (3.22.1)
Requirement already satisfied: asgiref==3.5.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 14)) (3.5.2)
Requirement already satisfied: async-generator==1.10 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 15)) (1.10)
Requirement already satisfied: attmap==0.13.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 17)) (0.13.2)
Requirement already satisfied: attrs==21.4.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 18)) (21.4.0)
Requirement already satisfied: babel==2.10.3 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 19)) (2.10.3)
Requirement already satisfied: bagit-profile==1.3.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 20)) (1.3.1)
Requirement already satisfied: bagit==1.8.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 21)) (1.8.1)
Requirement already satisfied: bcrypt==3.2.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 22)) (3.2.2)
Requirement already satisfied: bdbag==1.6.3 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 23)) (1.6.3)
Requirement already satisfied: beaker==1.11.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 24)) (1.11.0)
Requirement already satisfied: billiard==3.6.4.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 25)) (3.6.4.0)
Requirement already satisfied: bioblend==0.17.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 26)) (0.17.0)
Requirement already satisfied: black==22.3.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 27)) (22.3.0)
Requirement already satisfied: bleach==5.0.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 28)) (5.0.0)
Requirement already satisfied: boltons==21.0.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 29)) (21.0.0)
Requirement already satisfied: boto==2.49.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 30)) (2.49.0)
Requirement already satisfied: bx-python==0.8.13 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 31)) (0.8.13)
Requirement already satisfied: cachecontrol==0.12.11 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 32)) (0.12.11)
Requirement already satisfied: cached-property==1.5.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 33)) (1.5.2)
Requirement already satisfied: celery==5.2.7 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 34)) (5.2.7)
Requirement already satisfied: certifi==2022.6.15 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 35)) (2022.6.15)
Requirement already satisfied: cffi==1.15.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 36)) (1.15.0)
Requirement already satisfied: charset-normalizer==2.0.12 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 37)) (2.0.12)
Requirement already satisfied: cheetah3==3.2.6.post1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 38)) (3.2.6.post1)
Requirement already satisfied: circus==0.17.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 39)) (0.17.1)
Requirement already satisfied: click-didyoumean==0.3.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 40)) (0.3.0)
Requirement already satisfied: click-plugins==1.1.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 41)) (1.1.1)
Requirement already satisfied: click-repl==0.2.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 42)) (0.2.0)
Requirement already satisfied: click==8.1.3 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 43)) (8.1.3)
Requirement already satisfied: cloudauthz==0.6.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 44)) (0.6.0)
Requirement already satisfied: cloudbridge==3.0.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 45)) (3.0.0)
Requirement already satisfied: coloredlogs==15.0.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 47)) (15.0.1)
Requirement already satisfied: commonmark==0.9.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 48)) (0.9.1)
Requirement already satisfied: coverage==6.4.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 49)) (6.4.1)
Requirement already satisfied: cryptography==37.0.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 50)) (37.0.2)
Requirement already satisfied: cwltest==2.2.20210901154959 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 51)) (2.2.20210901154959)
Requirement already satisfied: cwltool==3.1.20211107152837 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 52)) (3.1.20211107152837)
Requirement already satisfied: cycler==0.11.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 53)) (0.11.0)
Requirement already satisfied: darker==1.5.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 54)) (1.5.0)
Requirement already satisfied: decorator==5.1.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 55)) (5.1.1)
Requirement already satisfied: defusedxml==0.7.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 56)) (0.7.1)
Requirement already satisfied: deprecated==1.2.13 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 57)) (1.2.13)
Requirement already satisfied: deprecation==2.1.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 58)) (2.1.0)
Requirement already satisfied: dictobj==0.4 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 59)) (0.4)
Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 60)) (0.6.2)
Requirement already satisfied: docutils==0.16 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 61)) (0.16)
Requirement already satisfied: ecdsa==0.17.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 62)) (0.17.0)
Requirement already satisfied: edam-ontology==1.25.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 63)) (1.25.2)
Requirement already satisfied: fastapi-utils==0.2.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 64)) (0.2.1)
Requirement already satisfied: fastapi==0.78.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 65)) (0.78.0)
Requirement already satisfied: fluent-logger==0.10.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 66)) (0.10.0)
Requirement already satisfied: fonttools==4.33.3 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 67)) (4.33.3)
Requirement already satisfied: fs==2.4.16 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 68)) (2.4.16)
Requirement already satisfied: funcsigs==1.0.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 69)) (1.0.2)
Requirement already satisfied: future==0.18.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 70)) (0.18.2)
Requirement already satisfied: galaxy-sequence-utils==1.1.5 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 71)) (1.1.5)
Requirement already satisfied: gravity==0.13.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 72)) (0.13.1)
Requirement already satisfied: greenlet==1.1.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 73)) (1.1.2)
Requirement already satisfied: gunicorn==20.1.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 74)) (20.1.0)
Requirement already satisfied: gxformat2==0.15.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 75)) (0.15.0)
Requirement already satisfied: h11==0.12.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 76)) (0.12.0)
Requirement already satisfied: h5py==3.7.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 77)) (3.7.0)
Requirement already satisfied: httpcore==0.15.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 78)) (0.15.0)
Requirement already satisfied: httpx==0.23.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 79)) (0.23.0)
Requirement already satisfied: humanfriendly==10.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 80)) (10.0)
Requirement already satisfied: idna==3.3 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 81)) (3.3)
Requirement already satisfied: imagesize==1.3.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 82)) (1.3.0)
Requirement already satisfied: importlib-metadata==4.11.4 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 83)) (4.11.4)
Requirement already satisfied: importlib-resources==5.8.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 84)) (5.8.0)
Requirement already satisfied: iniconfig==1.1.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 85)) (1.1.1)
Requirement already satisfied: isa-rwval==0.10.10 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 86)) (0.10.10)
Requirement already satisfied: isodate==0.6.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 87)) (0.6.1)
Requirement already satisfied: isort==5.10.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 88)) (5.10.1)
Requirement already satisfied: jinja2==3.1.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 89)) (3.1.2)
Requirement already satisfied: jsonref==0.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 90)) (0.2)
Requirement already satisfied: jsonschema==4.6.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 91)) (4.6.0)
Requirement already satisfied: junit-xml==1.9 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 92)) (1.9)
Requirement already satisfied: kiwisolver==1.4.3 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 93)) (1.4.3)
Requirement already satisfied: kombu==5.2.4 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 94)) (5.2.4)
Requirement already satisfied: lagom==1.7.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 95)) (1.7.1)
Requirement already satisfied: lockfile==0.12.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 96)) (0.12.2)
Requirement already satisfied: lxml==4.9.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 97)) (4.9.0)
Requirement already satisfied: mako==1.2.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 98)) (1.2.0)
Requirement already satisfied: markdown-it-reporter==0.0.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 99)) (0.0.2)
Requirement already satisfied: markdown==3.3.7 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 100)) (3.3.7)
Requirement already satisfied: markupsafe==2.1.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 101)) (2.1.1)
Requirement already satisfied: matplotlib==3.5.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 102)) (3.5.2)
Requirement already satisfied: mercurial==6.1.4 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 103)) (6.1.4)
Requirement already satisfied: mirakuru==2.4.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 104)) (2.4.2)
Requirement already satisfied: mistune==0.8.4 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 105)) (0.8.4)
Requirement already satisfied: mrcfile==1.3.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 106)) (1.3.0)
Requirement already satisfied: msgpack==1.0.4 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 107)) (1.0.4)
Requirement already satisfied: mypy-extensions==0.4.3 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 108)) (0.4.3)
Requirement already satisfied: networkx==2.5 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 109)) (2.5)
Requirement already satisfied: nodeenv==1.6.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 110)) (1.6.0)
Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 111)) (1.3.7)
Requirement already satisfied: nosehtml==0.4.6 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 112)) (0.4.6)
Requirement already satisfied: numpy==1.21.6 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 113)) (1.21.6)
Requirement already satisfied: oauthlib==3.2.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 114)) (3.2.0)
Requirement already satisfied: outcome==1.2.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 115)) (1.2.0)
Requirement already satisfied: oyaml==1.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 116)) (1.0)
Requirement already satisfied: packaging==21.3 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 117)) (21.3)
Requirement already satisfied: paramiko==2.11.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 118)) (2.11.0)
Requirement already satisfied: parsley==1.3 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 119)) (1.3)
Requirement already satisfied: paste==3.5.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 120)) (3.5.0)
Requirement already satisfied: pastedeploy==2.1.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 121)) (2.1.1)
Requirement already satisfied: pathspec==0.9.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 122)) (0.9.0)
Requirement already satisfied: pbr==5.9.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 123)) (5.9.0)
Requirement already satisfied: pebble==4.6.3 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 124)) (4.6.3)
Requirement already satisfied: pillow==9.1.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 125)) (9.1.1)
Requirement already satisfied: platformdirs==2.5.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 126)) (2.5.2)
Requirement already satisfied: pluggy==1.0.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 127)) (1.0.0)
Requirement already satisfied: port-for==0.6.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 128)) (0.6.2)
Requirement already satisfied: prettytable==3.3.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 129)) (3.3.0)
Requirement already satisfied: prompt-toolkit==3.0.29 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 130)) (3.0.29)
Requirement already satisfied: prov==1.5.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 131)) (1.5.1)
Requirement already satisfied: psutil==5.9.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 132)) (5.9.1)
Requirement already satisfied: pulsar-galaxy-lib==0.14.13 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 133)) (0.14.13)
Requirement already satisfied: pyasn1==0.4.8 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 135)) (0.4.8)
Requirement already satisfied: pycparser==2.21 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 136)) (2.21)
Requirement already satisfied: pycryptodome==3.14.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 137)) (3.14.1)
Requirement already satisfied: pydantic==1.9.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 138)) (1.9.1)
Requirement already satisfied: pydot==1.4.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 139)) (1.4.2)
Requirement already satisfied: pyeventsystem==0.1.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 140)) (0.1.0)
Requirement already satisfied: pyfaidx==0.7.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 141)) (0.7.0)
Requirement already satisfied: pygithub==1.55 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 142)) (1.55)
Requirement already satisfied: pygments==2.12.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 143)) (2.12.0)
Requirement already satisfied: pyjwt==2.4.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 144)) (2.4.0)
Requirement already satisfied: pykwalify==1.8.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 145)) (1.8.0)
Requirement already satisfied: pylibmagic==0.2.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 146)) (0.2.0)
Requirement already satisfied: pynacl==1.5.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 147)) (1.5.0)
Requirement already satisfied: pyopenssl==22.0.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 148)) (22.0.0)
Requirement already satisfied: pyparsing==3.0.9 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 149)) (3.0.9)
Requirement already satisfied: pyrsistent==0.18.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 152)) (0.18.1)
Requirement already satisfied: pysam==0.19.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 153)) (0.19.1)
Requirement already satisfied: pysocks==1.7.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 154)) (1.7.1)
Requirement already satisfied: pytest-asyncio==0.18.3 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 155)) (0.18.3)
Requirement already satisfied: pytest-celery==0.0.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 156)) (0.0.0)
Requirement already satisfied: pytest-cov==3.0.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 157)) (3.0.0)
Requirement already satisfied: pytest-html==3.1.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 158)) (3.1.1)
Requirement already satisfied: pytest-json-report==1.5.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 159)) (1.5.0)
Requirement already satisfied: pytest-metadata==2.0.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 160)) (2.0.1)
Requirement already satisfied: pytest-mock==3.7.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 161)) (3.7.0)
Requirement already satisfied: pytest-postgresql==4.1.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 162)) (4.1.1)
Requirement already satisfied: pytest-shard==0.1.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 163)) (0.1.2)
Requirement already satisfied: pytest==7.1.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 164)) (7.1.2)
Requirement already satisfied: python-dateutil==2.8.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 165)) (2.8.2)
Requirement already satisfied: python-irodsclient==1.1.3 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 166)) (1.1.3)
Requirement already satisfied: python-jose==3.3.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 167)) (3.3.0)
Requirement already satisfied: python-magic==0.4.27 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 168)) (0.4.27)
Requirement already satisfied: python-multipart==0.0.5 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 169)) (0.0.5)
Requirement already satisfied: python3-openid==3.2.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 170)) (3.2.0)
Requirement already satisfied: pytz==2022.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 171)) (2022.1)
Requirement already satisfied: pyyaml==6.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 172)) (6.0)
Requirement already satisfied: pyzmq==23.1.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 173)) (23.1.0)
Requirement already satisfied: rdflib==6.0.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 174)) (6.0.2)
Requirement already satisfied: recommonmark==0.7.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 175)) (0.7.1)
Requirement already satisfied: refgenconf==0.12.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 176)) (0.12.2)
Requirement already satisfied: repoze.lru==0.7 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 177)) (0.7)
Requirement already satisfied: requests-oauthlib==1.3.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 178)) (1.3.1)
Requirement already satisfied: requests-toolbelt==0.9.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 179)) (0.9.1)
Requirement already satisfied: requests==2.28.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 180)) (2.28.0)
Requirement already satisfied: responses==0.21.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 181)) (0.21.0)
Requirement already satisfied: rfc3986==1.5.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 182)) (1.5.0)
Requirement already satisfied: rich==12.4.4 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 183)) (12.4.4)
Requirement already satisfied: routes==2.5.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 184)) (2.5.1)
Requirement already satisfied: rsa==4.8 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 185)) (4.8)
Requirement already satisfied: ruamel.yaml.clib==0.2.6 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 186)) (0.2.6)
Requirement already satisfied: ruamel.yaml==0.17.17 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 187)) (0.17.17)
Requirement already satisfied: schema-salad==8.3.20220525163636 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 188)) (8.3.20220525163636)
Requirement already satisfied: scipy==1.7.3 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 189)) (1.7.3)
Requirement already satisfied: selenium==4.2.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 190)) (4.2.0)
Requirement already satisfied: setuptools-scm==5.0.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 191)) (5.0.2)
Requirement already satisfied: shellescape==3.8.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 192)) (3.8.1)
Requirement already satisfied: six==1.16.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 193)) (1.16.0)
Requirement already satisfied: sniffio==1.2.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 194)) (1.2.0)
Requirement already satisfied: snowballstemmer==2.2.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 195)) (2.2.0)
Requirement already satisfied: social-auth-core==4.0.3 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 196)) (4.0.3)
Requirement already satisfied: sortedcontainers==2.4.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 197)) (2.4.0)
Requirement already satisfied: sphinx-markdown-tables==0.0.15 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 198)) (0.0.15)
Requirement already satisfied: sphinx-rtd-theme==1.0.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 199)) (1.0.0)
Requirement already satisfied: sphinx==5.0.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 200)) (5.0.2)
Requirement already satisfied: sphinxcontrib-applehelp==1.0.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 201)) (1.0.2)
Requirement already satisfied: sphinxcontrib-devhelp==1.0.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 202)) (1.0.2)
Requirement already satisfied: sphinxcontrib-htmlhelp==2.0.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 203)) (2.0.0)
Requirement already satisfied: sphinxcontrib-jsmath==1.0.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 204)) (1.0.1)
Requirement already satisfied: sphinxcontrib-qthelp==1.0.3 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 205)) (1.0.3)
Requirement already satisfied: sphinxcontrib-serializinghtml==1.1.5 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 206)) (1.1.5)
Requirement already satisfied: sqlalchemy-migrate==0.13.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 207)) (0.13.0)
Requirement already satisfied: sqlalchemy==1.4.37 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 208)) (1.4.37)
Requirement already satisfied: sqlitedict==2.0.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 209)) (2.0.0)
Requirement already satisfied: sqlparse==0.4.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 210)) (0.4.2)
Requirement already satisfied: starlette-context==0.3.3 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 211)) (0.3.3)
Requirement already satisfied: starlette==0.19.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 212)) (0.19.1)
Requirement already satisfied: statsd==3.3.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 213)) (3.3.0)
Requirement already satisfied: supervisor==4.2.4 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 214)) (4.2.4)
Requirement already satisfied: svgwrite==1.4.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 215)) (1.4.2)
Requirement already satisfied: tempita==0.5.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 216)) (0.5.2)
Requirement already satisfied: tenacity==8.0.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 217)) (8.0.1)
Requirement already satisfied: testfixtures==6.18.5 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 218)) (6.18.5)
Requirement already satisfied: tifffile==2021.11.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 219)) (2021.11.2)
Requirement already satisfied: tinydb==4.7.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 220)) (4.7.0)
Requirement already satisfied: toml==0.10.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 221)) (0.10.2)
Requirement already satisfied: tomli==2.0.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 222)) (2.0.1)
Requirement already satisfied: tornado==6.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 223)) (6.1)
Requirement already satisfied: tqdm==4.64.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 224)) (4.64.0)
Requirement already satisfied: trio-websocket==0.9.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 225)) (0.9.2)
Requirement already satisfied: trio==0.21.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 226)) (0.21.0)
Requirement already satisfied: tuspy==0.2.5 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 227)) (0.2.5)
Requirement already satisfied: tuswsgi==0.5.4 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 228)) (0.5.4)
Requirement already satisfied: twill==3.0.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 229)) (3.0.2)
Requirement already satisfied: typed-ast==1.5.4 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 230)) (1.5.4)
Requirement already satisfied: typing-extensions==4.2.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 231)) (4.2.0)
Requirement already satisfied: tzlocal==2.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 232)) (2.1)
Requirement already satisfied: ubiquerg==0.6.2 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 233)) (0.6.2)
Requirement already satisfied: urllib3==1.26.9 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 234)) (1.26.9)
Requirement already satisfied: uvicorn==0.17.6 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 235)) (0.17.6)
Requirement already satisfied: uvloop==0.16.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 236)) (0.16.0)
Requirement already satisfied: vine==5.0.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 237)) (5.0.0)
Requirement already satisfied: watchdog==2.1.9 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 238)) (2.1.9)
Requirement already satisfied: wcwidth==0.2.5 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 239)) (0.2.5)
Requirement already satisfied: webencodings==0.5.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 240)) (0.5.1)
Requirement already satisfied: webob==1.8.7 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 241)) (1.8.7)
Requirement already satisfied: whoosh==2.7.4 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 242)) (2.7.4)
Requirement already satisfied: wrapt==1.14.1 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 243)) (1.14.1)
Requirement already satisfied: wsproto==1.1.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 244)) (1.1.0)
Requirement already satisfied: yacman==0.8.4 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 245)) (0.8.4)
Requirement already satisfied: zipp==3.8.0 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 246)) (3.8.0)
Requirement already satisfied: zipstream-new==1.1.8 in ./.venv/lib/python3.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 247)) (1.1.8)
Requirement already satisfied: setuptools in ./.venv/lib/python3.7/site-packages (from cwltool==3.1.20211107152837->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 52)) (47.1.0)
Requirement already satisfied: py>=1.8.2 in ./.venv/lib/python3.7/site-packages (from pytest==7.1.2->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 164)) (1.11.0)
WARNING: You are using pip version 22.0.4; however, version 22.1.2 is available.
You should consider upgrading via the '/home/ubuntu/galaxy/.venv/bin/python3 -m pip install --upgrade pip' command.
The Galaxy client has not yet been built and will be built now.
yarn install v1.22.19
[1/4] Resolving packages...
warning Resolution field "chokidar@3.5.3" is incompatible with requested version "chokidar@^2.0.0"
success Already up-to-date.
Done in 12.49s.
yarn run v1.22.19
$ NODE_ENV=production gulp && yarn run webpack-production-maps && yarn run save-build-hash
[21:18:34] Using gulpfile ~/galaxy/client/gulpfile.js
[21:18:34] Starting 'default'...
[21:18:34] Starting 'fonts'...
[21:18:34] Starting 'stageLibs'...
[21:18:34] Starting 'buildPlugins'...
[21:18:34] Finished 'stageLibs' after 62 ms
[21:18:34] Finished 'buildPlugins' after 94 ms
[21:18:34] Starting 'cleanPlugins'...
[21:18:34] Finished 'fonts' after 134 ms
No changes detected for annotate_image
No changes detected for chiraviz
No changes detected for cytoscape
No changes detected for drawrna
No changes detected for editor
No changes detected for example
No changes detected for heatmap_default
No changes detected for hyphyvision
No changes detected for jqplot_bar
No changes detected for media_player
No changes detected for mvpapp
No changes detected for ngl
No changes detected for nora
No changes detected for nvd3_bar
No changes detected for openlayers
No changes detected for openseadragon
No changes detected for PCA_3Dplot
No changes detected for phylocanvas
No changes detected for pv
No changes detected for venn
No changes detected for new_user
[21:18:35] Finished 'cleanPlugins' after 1.25 s
[21:18:35] Starting 'stagePlugins'...
[21:18:38] Finished 'stagePlugins' after 2.89 s
[21:18:38] Finished 'default' after 4.25 s
$ GXY_BUILD_SOURCEMAPS=1 NODE_ENV=production webpack
Browserslist: caniuse-lite is outdated. Please run:
  npx browserslist@latest --update-db
  Why you should do it regularly: https://github.com/browserslist/browserslist#browsers-data-updating
^C
~/galaxy$ npx browserslist@latest --update-db
npx browserslist@latest --update-db
npx: installed 7 in 1.545s
Cannot find package.json. Is this the right directory to run `npx update-browserslist-db` in?

I tried troubleshooting using the advice I found on Stack Overflow but it still isn't working. @cannin @mil2041 I would appreciate any tips you may have for me!

sajo25 commented 2 years ago

We will use Docker instead of VirtualBox to set up a local Galaxy instance and install the netboxr tool from the ToolShed.