forgetfr
commented
3 years ago I do have the same error. Its seems the installation of attmap use "use_2to3" which is no more supported by "python3-setuptools" since version 58.0.0 (https://setuptools.readthedocs.io/en/latest/history.html#v58-0-0)
python3-setuptools is installed by compose/galaxy-server/Dockerfile on line 113.
I'm trying to change the Dockerfile to install version. 57.5.0. But, I don't know how to do it.
bgruening
Hello,
I've tried this in a fresh updated RH7, RH8 and Ubuntu Server 21.04 installation: Under my user's home (which is part of docker group) I've created a directory called /home/user/galaxy/. I fetched from git the docker-galaxy-stable compose directory. Inside the directory, I executed docker-compuse up -d.
At one point I get this same message in RH7 and RH8 (see below). Any ideas?
Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample Initializing static/welcome.html from welcome.html.sample Creating Python virtual environment for Galaxy: /galaxy/.venv using Python: python3 To avoid this, use the --no-create-venv flag or set $GALAXY_VIRTUAL_ENV to an existing environment before starting Galaxy. Fetching https://files.pythonhosted.org/packages/source/v/virtualenv/virtualenv-16.7.9.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 5001k 100 5001k 0 0 11.4M 0 --:--:-- --:--:-- --:--:-- 23.7M Verifying /tmp/galaxy-virtualenv-karfCA/virtualenv-16.7.9.tar.gz checksum is 0d62c70883c0342d59c11d0ddac0d954d0431321a41ab20851facf2b222598f3 Using base prefix '/usr' New python executable in /galaxy/.venv/bin/python3 Also creating executable in /galaxy/.venv/bin/python Installing setuptools, pip, wheel... done. Activating virtualenv at /galaxy/.venv Requirement already satisfied: pip>=8.1 in ./.venv/lib/python3.8/site-packages (21.2.4) 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 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 Downloading adal-1.2.4-py2.py3-none-any.whl (55 kB) Collecting amqp==2.6.0 Downloading amqp-2.6.0-py2.py3-none-any.whl (47 kB) Collecting appdirs==1.4.4 Downloading appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB) Collecting attmap==0.12.11 Downloading attmap-0.12.11.tar.gz (9.9 kB) ERROR: Command errored out with exit status 1: command: /galaxy/.venv/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-edptk05l/attmap_6f11a2915a13410aa29fe4836d140c48/setup.py'"'"'; file='"'"'/tmp/pip-install-edptk05l/attmap_6f11a2915a13410aa29fe4836d140c48/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-zdxx1rfb cwd: /tmp/pip-install-edptk05l/attmap_6f11a2915a13410aa29fe4836d140c48/ Complete output (1 lines): error in attmap setup command: use_2to3 is invalid.
WARNING: Discarding https://files.pythonhosted.org/packages/d0/d4/8b8fca155270a6675bac9a1e49b7c616ae763f66af7b836042ecfc805552/attmap-0.12.11.tar.gz#sha256=95b1f7dbcdad7278a3702fa921be6271046c96e1c9ed9feb10e0d4c13092b0a0 (from https://pypi.org/simple/attmap/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Could not find a version that satisfies the requirement attmap==0.12.11 (from versions: 0.1, 0.1.1, 0.1.2, 0.1.4, 0.1.5, 0.1.6, 0.1.7, 0.1.8, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.10, 0.11, 0.12, 0.12.1, 0.12.2, 0.12.3, 0.12.4, 0.12.5, 0.12.6, 0.12.7, 0.12.8, 0.12.9, 0.12.10, 0.12.11, 0.13.0) ERROR: No matching distribution found for attmap==0.12.11 The command '/bin/sh -c apt update && apt install --no-install-recommends libcurl4-openssl-dev libssl-dev python3-dev python3-pip -y && update-alternatives --install /usr/bin/python python /usr/bin/python3 9 && mkdir "${GALAXY_ROOT}" && curl -L -s $GALAXY_REPO/archive/$GALAXY_RELEASE.tar.gz | tar xzf - --strip-components=1 -C $GALAXY_ROOT && cd $GALAXY_ROOT && ./scripts/common_startup.sh && . $GALAXY_ROOT/.venv/bin/activate && pip3 install drmaa psycopg2 pycurl pykube && pip3 install importlib-metadata importlib-resources pathlib2 ruamel.yaml.clib typing zipp && deactivate && rm -rf .ci .circleci .coveragerc .gitignore .travis.yml CITATION CODE_OF_CONDUCT.md CONTRIBUTING.md CONTRIBUTORS.md LICENSE.txt Makefile README.rst SECURITY_POLICY.md pytest.ini tox.ini client contrib doc config/plugins lib/galaxy_test test test-data .venv/lib/node_modules .venv/src/node-v10.15.3-linux-x64 .venv/include/node .venv/bin/node .venv/bin/nodeenv && /usr/bin/common_cleanup.sh' returned a non-zero code: 1 ERROR: Service 'galaxy-server' failed to build : Build failed