Question: How to deal with PROXY when installing new local instance
0
christophe.habib • 340 wrote:
Hello,
I am trying to install a new local instance of galaxy. So I did as always :
git clone -b release_16.10 https://github.com/galaxyproject/galaxy.git
./run.sh
And I have this error related to proxy :
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| ./run.sh | |
| Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample | |
| Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample | |
| Initializing config/shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample | |
| Initializing config/shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample | |
| 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 tool-data/shared/ucsc/ucsc_build_sites.txt from ucsc_build_sites.txt.sample | |
| Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample | |
| Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample | |
| Initializing static/welcome.html from welcome.html.sample | |
| Running virtualenv with interpreter /usr/bin/python2.7 | |
| New python executable in /home/username/GalaxLocal/galaxy/.venv/bin/python2.7 | |
| Also creating executable in /home/username/GalaxLocal/galaxy/.venv/bin/python | |
| Installing setuptools, pip, wheel...done. | |
| Activating virtualenv at .venv | |
| Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages | |
| Collecting bx-python==0.7.3 (from -r requirements.txt (line 2)) | |
| Exception: | |
| Traceback (most recent call last): | |
| File "/home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/basecommand.py", line 215, in main | |
| status = self.run(options, args) | |
| File "/home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/commands/install.py", line 335, in run | |
| wb.build(autobuilding=True) | |
| File "/home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/wheel.py", line 749, in build | |
| self.requirement_set.prepare_files(self.finder) | |
| File "/home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/req/req_set.py", line 380, in prepare_files | |
| ignore_dependencies=self.ignore_dependencies)) | |
| File "/home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/req/req_set.py", line 554, in _prepare_file | |
| require_hashes | |
| File "/home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/req/req_install.py", line 278, in populate_link | |
| self.link = finder.find_requirement(self, upgrade) | |
| File "/home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/index.py", line 465, in find_requirement | |
| all_candidates = self.find_all_candidates(req.name) | |
| File "/home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/index.py", line 423, in find_all_candidates | |
| for page in self._get_pages(url_locations, project_name): | |
| File "/home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/index.py", line 568, in _get_pages | |
| page = self._get_page(location) | |
| File "/home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/index.py", line 683, in _get_page | |
| return HTMLPage.get_page(link, session=self.session) | |
| File "/home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/index.py", line 792, in get_page | |
| "Cache-Control": "max-age=600", | |
| File "/home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/sessions.py", line 488, in get | |
| return self.request('GET', url, **kwargs) | |
| File "/home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/download.py", line 386, in request | |
| return super(PipSession, self).request(method, url, *args, **kwargs) | |
| File "/home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/sessions.py", line 475, in request | |
| resp = self.send(prep, **send_kwargs) | |
| File "/home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/sessions.py", line 596, in send | |
| r = adapter.send(request, **kwargs) | |
| File "/home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/cachecontrol/adapter.py", line 47, in send | |
| resp = super(CacheControlAdapter, self).send(request, **kw) | |
| File "/home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/adapters.py", line 390, in send | |
| conn = self.get_connection(request.url, proxies) | |
| File "/home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/adapters.py", line 290, in get_connection | |
| proxy_manager = self.proxy_manager_for(proxy) | |
| File "/home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/adapters.py", line 184, in proxy_manager_for | |
| **proxy_kwargs | |
| File "/home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/adapters.py", line 43, in SOCKSProxyManager | |
| raise InvalidSchema("Missing dependencies for SOCKS support.") | |
| InvalidSchema: Missing dependencies for SOCKS support. |
I can have a workaround by doing : export all_proxy="https://adress_proxy:port/"
So here the wheels things are running for some package such as PyYAML, numpy etc. But It still crash for repoze package.
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| chabib@chabib-HP-EliteDesk-705-G1-MT:~/Documents/GalaxLocal/galaxy$ ./run.sh | |
| Activating virtualenv at .venv | |
| Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages | |
| Collecting bx-python==0.7.3 (from -r requirements.txt (line 2)) | |
| /home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:318: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/security.html#snimissingwarning. | |
| SNIMissingWarning | |
| /home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:122: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/security.html#insecureplatformwarning. | |
| InsecurePlatformWarning | |
| Downloading https://wheels.galaxyproject.org/packages/bx_python-0.7.3-cp27-cp27mu-manylinux1_x86_64.whl (2.1MB) | |
| 100% |████████████████████████████████| 2.2MB 1.3MB/s | |
| Collecting MarkupSafe==0.23 (from -r requirements.txt (line 3)) | |
| Downloading https://wheels.galaxyproject.org/packages/MarkupSafe-0.23-cp27-cp27mu-manylinux1_x86_64.whl | |
| Collecting PyYAML==3.11 (from -r requirements.txt (line 4)) | |
| Downloading https://wheels.galaxyproject.org/packages/PyYAML-3.11-cp27-cp27mu-manylinux1_x86_64.whl (367kB) | |
| 100% |████████████████████████████████| 368kB 632kB/s | |
| Collecting SQLAlchemy==1.0.15 (from -r requirements.txt (line 5)) | |
| Downloading https://wheels.galaxyproject.org/packages/SQLAlchemy-1.0.15-cp27-cp27mu-manylinux1_x86_64.whl (1.0MB) | |
| 100% |████████████████████████████████| 1.0MB 626kB/s | |
| Collecting mercurial==3.7.3 (from -r requirements.txt (line 6)) | |
| Downloading https://wheels.galaxyproject.org/packages/mercurial-3.7.3-cp27-cp27mu-manylinux1_x86_64.whl (1.5MB) | |
| 100% |████████████████████████████████| 1.5MB 618kB/s | |
| Collecting numpy==1.9.2 (from -r requirements.txt (line 7)) | |
| Downloading https://wheels.galaxyproject.org/packages/numpy-1.9.2-cp27-cp27mu-manylinux1_x86_64.whl (10.2MB) | |
| 100% |████████████████████████████████| 10.2MB 776kB/s | |
| Collecting pycrypto==2.6.1 (from -r requirements.txt (line 8)) | |
| Downloading https://wheels.galaxyproject.org/packages/pycrypto-2.6.1-cp27-cp27mu-manylinux1_x86_64.whl (492kB) | |
| 100% |████████████████████████████████| 501kB 636kB/s | |
| Collecting Paste==2.0.2 (from -r requirements.txt (line 15)) | |
| Downloading https://wheels.galaxyproject.org/packages/Paste-2.0.2-py2-none-any.whl (610kB) | |
| 100% |████████████████████████████████| 614kB 1.2MB/s | |
| Collecting PasteDeploy==1.5.2 (from -r requirements.txt (line 16)) | |
| Downloading https://wheels.galaxyproject.org/packages/PasteDeploy-1.5.2-py2.py3-none-any.whl | |
| Collecting docutils==0.12 (from -r requirements.txt (line 17)) | |
| Downloading https://wheels.galaxyproject.org/packages/docutils-0.12-py2-none-any.whl (509kB) | |
| 100% |████████████████████████████████| 512kB 631kB/s | |
| Collecting wchartype==0.1 (from -r requirements.txt (line 18)) | |
| Downloading https://wheels.galaxyproject.org/packages/wchartype-0.1-py2-none-any.whl | |
| Collecting repoze.lru==0.6 (from -r requirements.txt (line 19)) | |
| /home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:122: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/security.html#insecureplatformwarning. | |
| InsecurePlatformWarning | |
| Retrying (Retry(total=4, connect=None, read=None, redirect=None)) after connection broken by 'ProxyError('Cannot connect to proxy.', error(104, 'Connexion r\xc3\xa9-initialis\xc3\xa9e par le correspondant'))': http://pypi.python.org/simple/repoze-lru/ | |
| /home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:122: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/security.html#insecureplatformwarning. | |
| InsecurePlatformWarning | |
| Retrying (Retry(total=3, connect=None, read=None, redirect=None)) after connection broken by 'ProxyError('Cannot connect to proxy.', error(104, 'Connexion r\xc3\xa9-initialis\xc3\xa9e par le correspondant'))': http://pypi.python.org/simple/repoze-lru/ | |
| /home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:122: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/security.html#insecureplatformwarning. | |
| InsecurePlatformWarning | |
| Retrying (Retry(total=2, connect=None, read=None, redirect=None)) after connection broken by 'ProxyError('Cannot connect to proxy.', error(104, 'Connexion r\xc3\xa9-initialis\xc3\xa9e par le correspondant'))': http://pypi.python.org/simple/repoze-lru/ | |
| /home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:122: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/security.html#insecureplatformwarning. | |
| InsecurePlatformWarning | |
| Retrying (Retry(total=1, connect=None, read=None, redirect=None)) after connection broken by 'ProxyError('Cannot connect to proxy.', error(104, 'Connexion r\xc3\xa9-initialis\xc3\xa9e par le correspondant'))': http://pypi.python.org/simple/repoze-lru/ | |
| /home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:122: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/security.html#insecureplatformwarning. | |
| InsecurePlatformWarning | |
| Retrying (Retry(total=0, connect=None, read=None, redirect=None)) after connection broken by 'ProxyError('Cannot connect to proxy.', error(104, 'Connexion r\xc3\xa9-initialis\xc3\xa9e par le correspondant'))': http://pypi.python.org/simple/repoze-lru/ | |
| /home/username/GalaxLocal/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:122: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/security.html#insecureplatformwarning. | |
| InsecurePlatformWarning | |
| Could not find a version that satisfies the requirement repoze.lru==0.6 (from -r requirements.txt (line 19)) (from versions: ) | |
| No matching distribution found for repoze.lru==0.6 (from -r requirements.txt (line 19)) |
And so the workaround wasn't a good solution. Obviously, I have the same error withcommon_startup.sh. So my question is simple :
When you work in an environment where every single request goes through a proxy (here, in a hospital), how can I set the proxy properly to make everything work at the first attempt ?
Thank you for your help !
On note : I have same kind of issues when I try to get docker version of Galaxy.