Hi,
I am trying to install Galaxy on my MAC and am getting the following errors on install:
Below is the log.
My Operating system is MAC OS Catalina 10.15.6 (19G73)
Thanks !
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Successfully built attmap bagit beaker cachecontrol dictobj dogpile.cache future prettytable pyperclip pyrsistent pysam pysftp pyyaml rdflib-jsonld refgenconf sqlalchemy-utils tempita ubiquerg warlock wrapt yacman scandir
Installing collected packages: six, python-dateutil, chardet, certifi, idna, urllib3, requests, pyjwt, pycparser, cffi, cryptography, adal, vine, amqp, appdirs, ubiquerg, attmap, attrs, azure-nspkg, azure-common, azure-cosmosdb-nspkg, futures, azure-storage-common, azure-cosmosdb-table, oauthlib, requests-oauthlib, isodate, msrest, msrestazure, azure-mgmt-nspkg, azure-mgmt-compute, azure-mgmt-devtestlabs, azure-mgmt-network, azure-mgmt-resource, azure-mgmt-storage, azure-storage-nspkg, azure-storage-blob, pytz, babel, bagit, bcrypt, tzlocal, setuptools-scm, bdbag, beaker, pyyaml, requests-toolbelt, boto, bioblend, webencodings, pyparsing, packaging, bleach, boltons, docutils, jmespath, botocore, s3transfer, boto3, numpy, bx-python, cachecontrol, cachetools, cheetah3, pbr, stevedore, pyperclip, wcwidth, cmd2, prettytable, cliff, cloudauthz, netaddr, rfc3986, oslo.i18n, wrapt, debtcollector, oslo.config, msgpack, iso8601, netifaces, oslo.utils, oslo.serialization, os-service-types, keystoneauth1, python-keystoneclient, pyasn1, rsa, pyasn1-modules, google-auth, uritemplate, httplib2, google-auth-httplib2, google-api-python-client, simplejson, deprecation, munch, decorator, requestsexceptions, dogpile.cache, jsonpointer, jsonpatch, openstacksdk, os-client-config, osc-lib, oslo.context, oslo.log, python-neutronclient, oauth2client, python-swiftclient, deprecated, pyeventsystem, tenacity, python-novaclient, pynacl, paramiko, pysftp, zipp, importlib-metadata, pyrsistent, jsonschema, warlock, pyopenssl, python-glanceclient, python-cinderclient, cloudbridge, humanfriendly, coloredlogs, psutil, shellescape, future, typing-extensions, lockfile, mistune, rdflib, ruamel.yaml.clib, ruamel.yaml, rdflib-jsonld, schema-salad, lxml, networkx, prov, pathlib2, mypy-extensions, scandir, cwltool, dictobj, docopt, ecdsa, fabric3, galaxy-sequence-utils, gxformat2, h5py, isa-rwval, kombu, markupsafe, mako, markdown, mercurial, monotonic, nodeenv, nose, oyaml, parsley, paste, pastedeploy, pastescript, webob, pulsar-galaxy-lib, pycryptodome, pykwalify, pysam, python-jose, pyuwsgi, tqdm, yacman, refgenconf, repoze.lru, routes, defusedxml, python3-openid, unidecode, social-auth-core, sortedcontainers, sqlalchemy, tempita, sqlparse, sqlalchemy-migrate, sqlalchemy-utils, svgwrite, whoosh
Successfully installed adal-1.2.3 amqp-2.5.2 appdirs-1.4.3 attmap-0.12.11 attrs-19.3.0 azure-common-1.1.14 azure-cosmosdb-nspkg-2.0.2 azure-cosmosdb-table-1.0.4 azure-mgmt-compute-4.0.1 azure-mgmt-devtestlabs-2.2.0 azure-mgmt-network-2.1.0 azure-mgmt-nspkg-3.0.2 azure-mgmt-resource-2.0.0 azure-mgmt-storage-2.0.0 azure-nspkg-3.0.2 azure-storage-blob-1.3.1 azure-storage-common-1.4.2 azure-storage-nspkg-3.1.0 babel-2.8.0 bagit-1.7.0 bcrypt-3.1.7 bdbag-1.5.6 beaker-1.11.0 bioblend-0.13.0 bleach-3.1.5 boltons-20.1.0 boto-2.49.0 boto3-1.9.114 botocore-1.12.253 bx-python-0.8.8 cachecontrol-0.11.7 cachetools-3.1.1 certifi-2020.4.5.1 cffi-1.14.0 chardet-3.0.4 cheetah3-3.2.4 cliff-2.18.0 cloudauthz-0.6.0 cloudbridge-2.0.0 cmd2-0.8.9 coloredlogs-14.0 cryptography-2.9.2 cwltool-1.0.20191225192155 debtcollector-1.22.0 decorator-4.4.2 defusedxml-0.7.0rc1 deprecated-1.2.9 deprecation-2.1.0 dictobj-0.4 docopt-0.6.2 docutils-0.15.2 dogpile.cache-0.9.1 ecdsa-0.15 fabric3-1.14.post1 future-0.18.2 futures-3.1.1 galaxy-sequence-utils-1.1.5 google-api-python-client-1.7.8 google-auth-1.14.1 google-auth-httplib2-0.0.3 gxformat2-0.11.3 h5py-2.10.0 httplib2-0.17.3 humanfriendly-8.2 idna-2.9 importlib-metadata-1.6.0 isa-rwval-0.10.7 iso8601-0.1.12 isodate-0.6.0 jmespath-0.9.5 jsonpatch-1.25 jsonpointer-2.0 jsonschema-3.2.0 keystoneauth1-4.0.0 kombu-4.6.8 lockfile-0.12.2 lxml-4.5.0 mako-1.1.2 markdown-3.1.1 markupsafe-1.1.1 mercurial-5.4 mistune-0.8.4 monotonic-1.5 msgpack-1.0.0 msrest-0.5.5 msrestazure-0.5.0 munch-2.5.0 mypy-extensions-0.4.3 netaddr-0.7.19 netifaces-0.10.9 networkx-1.11 nodeenv-1.3.5 nose-1.3.7 numpy-1.16.6 oauth2client-4.1.3 oauthlib-3.1.0 openstacksdk-0.17.0 os-client-config-2.1.0 os-service-types-1.7.0 osc-lib-2.0.0 oslo.config-7.0.0 oslo.context-2.23.0 oslo.i18n-3.25.1 oslo.log-3.45.2 oslo.serialization-2.29.2 oslo.utils-3.42.1 oyaml-0.9 packaging-20.3 paramiko-2.7.1 parsley-1.3 paste-3.4.0 pastedeploy-2.1.0 pastescript-3.2.0 pathlib2-2.3.5 pbr-5.4.5 prettytable-0.7.2 prov-1.5.1 psutil-5.7.0 pulsar-galaxy-lib-0.14.0.dev3 pyasn1-0.4.8 pyasn1-modules-0.2.8 pycparser-2.20 pycryptodome-3.9.7 pyeventsystem-0.1.0 pyjwt-1.7.1 pykwalify-1.7.0 pynacl-1.3.0 pyopenssl-19.1.0 pyparsing-2.4.7 pyperclip-1.8.0 pyrsistent-0.16.0 pysam-0.16.0.1 pysftp-0.2.9 python-cinderclient-4.0.0 python-dateutil-2.8.1 python-glanceclient-2.12.0 python-jose-3.1.0 python-keystoneclient-3.17.0 python-neutronclient-6.9.0 python-novaclient-11.0.0 python-swiftclient-3.6.0 python3-openid-3.2.0 pytz-2020.1 pyuwsgi-2.0.18.post0 pyyaml-5.3.1 rdflib-4.2.2 rdflib-jsonld-0.4.0 refgenconf-0.7.0 repoze.lru-0.7 requests-2.23.0 requests-oauthlib-1.3.0 requests-toolbelt-0.9.1 requestsexceptions-1.4.0 rfc3986-1.4.0 routes-2.4.1 rsa-4.0 ruamel.yaml-0.16.0 ruamel.yaml.clib-0.2.0 s3transfer-0.2.1 scandir-1.10.0 schema-salad-4.5.20191229160203 setuptools-scm-3.5.0 shellescape-3.4.1 simplejson-3.17.0 six-1.11.0 social-auth-core-3.3.0 sortedcontainers-2.1.0 sqlalchemy-1.3.16 sqlalchemy-migrate-0.13.0 sqlalchemy-utils-0.36.5 sqlparse-0.3.1 stevedore-1.32.0 svgwrite-1.3.1 tempita-0.5.2 tenacity-4.12.0 tqdm-4.46.0 typing-extensions-3.7.4.2 tzlocal-2.0.0 ubiquerg-0.5.1 unidecode-1.1.1 uritemplate-3.0.1 urllib3-1.25.9 vine-1.3.0 warlock-1.3.3 wcwidth-0.1.9 webencodings-0.5.1 webob-1.8.6 whoosh-2.7.4 wrapt-1.12.1 yacman-0.6.7 zipp-1.2.0
The Galaxy client has not yet been built and will be built now.
Installing node into /Users/georgeweingart/Documents/GW_Galaxy/galaxy/.venv with nodeenv.
- Install prebuilt node (10.15.3) .
Traceback (most recent call last):
File “/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py”, line 1317, in do_open
encode_chunked=req.has_header(‘Transfer-encoding’))
File “/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py”, line 1244, in request
self._send_request(method, url, body, headers, encode_chunked)
File “/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py”, line 1290, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File “/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py”, line 1239, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File “/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py”, line 1026, in _send_output
self.send(msg)
File “/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py”, line 966, in send
self.connect()
File “/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py”, line 1414, in connect
server_hostname=server_hostname)
File “/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py”, line 423, in wrap_socket
session=session
File “/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py”, line 870, in _create
self.do_handshake()
File “/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py”, line 1139, in do_handshake
self._sslobj.do_handshake()
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1076)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/Users/georgeweingart/Documents/GW_Galaxy/galaxy/.venv/bin/nodeenv”, line 8, in
sys.exit(main())
File “/Users/georgeweingart/Documents/GW_Galaxy/galaxy/.venv/lib/python3.7/site-packages/nodeenv.py”, line 1113, in main
create_environment(env_dir, opt)
File “/Users/georgeweingart/Documents/GW_Galaxy/galaxy/.venv/lib/python3.7/site-packages/nodeenv.py”, line 936, in create_environment
install_node(env_dir, src_dir, opt)
File “/Users/georgeweingart/Documents/GW_Galaxy/galaxy/.venv/lib/python3.7/site-packages/nodeenv.py”, line 700, in install_node
install_node_wrapped(env_dir, src_dir, opt)
File “/Users/georgeweingart/Documents/GW_Galaxy/galaxy/.venv/lib/python3.7/site-packages/nodeenv.py”, line 723, in install_node_wrapped
download_node_src(node_url, src_dir, opt, prefix)
File “/Users/georgeweingart/Documents/GW_Galaxy/galaxy/.venv/lib/python3.7/site-packages/nodeenv.py”, line 552, in download_node_src
dl_contents = io.BytesIO(urlopen(node_url).read())
File “/Users/georgeweingart/Documents/GW_Galaxy/galaxy/.venv/lib/python3.7/site-packages/nodeenv.py”, line 580, in urlopen
return urllib2.urlopen(req)
File “/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py”, line 222, in urlopen
return opener.open(url, data, timeout)
File “/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py”, line 525, in open
response = self._open(req, data)
File “/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py”, line 543, in _open
‘_open’, req)
File “/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py”, line 503, in _call_chain
result = func(*args)
File “/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py”, line 1360, in https_open
context=self._context, check_hostname=self._check_hostname)
File “/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py”, line 1319, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1076)>