Before installing my local Galaxy, I did this:
sudo add-apt-repository ppa:deadsnakes/ppa
sudo apt-get update
sudo apt-get install python3.6
sudo apt-get install python3.6-venv
python3.6 -m venv env_python36
source env_python36/bin/activate
pip install --upgrade pip
pip install requests[security]
pip install requests
Suggestion: change the version of setuptools at the requirements’ file.
pip install setuptools –upgrade
mkdir Galaxy
cd Galaxy
Download/copy of directory containing the Galaxy release
git clone -b release_20.01 GitHub - galaxyproject/galaxy: Data intensive science for everyone.
cd galaxy
cp config/galaxy.yml.sample config/galaxy.yml
Because I got an error during the installation, I fixed the uwsgi:
./.venv/bin/pip uninstall -y uwsgi && ./.venv/bin/pip install --no-cache-dir uwsgi==2.0.17
I ran the command:
sh run.sh
Installing the local Galaxy, release 20.01, I got this message at the end of the installation. I already have the bagit installed in my virtual environment.
Collecting bagit==1.7.0
Using cached bagit-1.7.0.tar.gz (28 kb)
ERROR: Command errored out with exit status 1:
command: /disk2/Users/FLIR/Galaxy/galaxy/.venv/bin/python3 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-g6p0egwj/bagit/setup.py'"'"'; __file__='"'"'/tmp/pip-install-g6p0egwj/bagit/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-install-g6p0egwj/bagit/pip-egg-info
cwd: /tmp/pip-install-g6p0egwj/bagit/
Complete output (26 lines):
Download error on https://pypi.python.org/simple/setuptools_scm/: hostname 'webproxy-na.dupont.com' doesn't match either of 'www.python.org', 'docs.python.org', 'bugs.python.org', 'wiki.python.org', 'hg.python.org', 'mail.python.org', 'pypi.python.org', 'packaging.python.org', 'login.python.org', 'discuss.python.org', 'us.pycon.org', 'pypi.io', 'docs.pypi.io', 'pypi.org', 'docs.pypi.org', 'donate.pypi.org', 'devguide.python.org', 'www.bugs.python.org', 'python.org' -- Some packages may not be found!
Download error on https://pypi.python.org/simple/setuptools-scm/: hostname 'webproxy-na.dupont.com' doesn't match either of 'www.python.org', 'docs.python.org', 'bugs.python.org', 'wiki.python.org', 'hg.python.org', 'mail.python.org', 'pypi.python.org', 'packaging.python.org', 'login.python.org', 'discuss.python.org', 'us.pycon.org', 'pypi.io', 'docs.pypi.io', 'pypi.org', 'docs.pypi.org', 'donate.pypi.org', 'devguide.python.org', 'www.bugs.python.org', 'python.org' -- Some packages may not be found!
Couldn't find index page for 'setuptools_scm' (maybe misspelled?)
Download error on https://pypi.python.org/simple/: hostname 'webproxy-na.dupont.com' doesn't match either of 'www.python.org', 'docs.python.org', 'bugs.python.org', 'wiki.python.org', 'hg.python.org', 'mail.python.org', 'pypi.python.org', 'packaging.python.org', 'login.python.org', 'discuss.python.org', 'us.pycon.org', 'pypi.io', 'docs.pypi.io', 'pypi.org', 'docs.pypi.org', 'donate.pypi.org', 'devguide.python.org', 'www.bugs.python.org', 'python.org' -- Some packages may not be found!
No local packages or download links found for setuptools-scm
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-install-g6p0egwj/bagit/setup.py", line 78, in <module>
"Programming Language :: Python :: 3.6",
File "/usr/local/lib/python3.5/distutils/core.py", line 108, in setup
_setup_distribution = dist = klass(attrs)
File "/disk2/Users/FLIR/Galaxy/galaxy/.venv/lib/python3.5/site-packages/setuptools/dist.py", line 239, in __init__
self.fetch_build_eggs(attrs.pop('setup_requires'))
File "/disk2/Users/FLIR/Galaxy/galaxy/.venv/lib/python3.5/site-packages/setuptools/dist.py", line 264, in fetch_build_eggs
replace_conflicting=True
File "/disk2/Users/FLIR/Galaxy/galaxy/.venv/lib/python3.5/site-packages/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, ws, installer)
File "/disk2/Users/FLIR/Galaxy/galaxy/.venv/lib/python3.5/site-packages/pkg_resources.py", line 818, in best_match
return self.obtain(req, installer) # try and download/install
File "/disk2/Users/FLIR/Galaxy/galaxy/.venv/lib/python3.5/site-packages/pkg_resources.py", line 830, in obtain
return installer(requirement)
File "/disk2/Users/FLIR/Galaxy/galaxy/.venv/lib/python3.5/site-packages/setuptools/dist.py", line 314, in fetch_build_egg
return cmd.easy_install(req)
File "/disk2/Users/FLIR/Galaxy/galaxy/.venv/lib/python3.5/site-packages/setuptools/command/easy_install.py", line 587, in easy_install
raise DistutilsError(msg)
distutils.errors.DistutilsError: Could not find suitable distribution for Requirement.parse('setuptools-scm')
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
Any suggestion to solve this?
Thank you in advance.
