Question: Galaxy Install Issues - pip version
0
gravatar for njoebott
2.1 years ago by
njoebott30
njoebott30 wrote:

I've tried to deploy/run Galaxy on two different OS's (CentOS7 and Ubuntu) with no success. Keep getting the following error:

Could not find a version that satisfies the requirement pip==8.0.2+gx2 (from versions: ) No matching distribution found for pip==8.0.2+gx2

Neither system had pip installed to begin with as I assumed the run.sh script would install the required dependencies. Both are running python version 2.7+.

Thanks in advance for any guidance.

Nathan

galaxy • 1.3k views
ADD COMMENTlink modified 10 weeks ago by guillaume.lhostis0 • written 2.1 years ago by njoebott30
0
gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

As it so happens, a live talk that involves pip set-up is live streaming right now from the GCC 2016 conference.

https://gcc16.sched.org/

Slides, talk videos, and more can be found on the website as a resource.

If you have problems after this, email the galaxy-dev@lists.galaxyproject.org mailing list.

Best, Jen, Galaxy team

ADD COMMENTlink written 2.1 years ago by Jennifer Hillman Jackson25k
0
gravatar for njoebott
2.1 years ago by
njoebott30
njoebott30 wrote:

Thanks Jen. I was able to successfully install pip. This time around I installed the latest version of pip directly first (from pypa.io) then ran the run.sh script. However, I quickly ran into another issue...more troubleshooting ahead....here's the details.

[root@galaxy1 galaxy]# curl "https://bootstrap.pypa.io/get-pip.py" -o "get-pip.py" % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 1488k 100 1488k 0 0 4188k 0 --:--:-- --:--:-- --:--:-- 4206k [root@galaxy1 galaxy]# python get-pip.py Collecting pip Downloading pip-8.1.2-py2.py3-none-any.whl (1.2MB) 100% |████████████████████████████████| 1.2MB 718kB/s Collecting wheel Downloading wheel-0.29.0-py2.py3-none-any.whl (66kB) 100% |████████████████████████████████| 71kB 7.5MB/s Installing collected packages: pip, wheel Successfully installed pip-8.1.2 wheel-0.29.0 [root@galaxy1 galaxy]# pip -V pip 8.1.2 from /usr/lib/python2.7/site-packages (python 2.7) [root@galaxy1 galaxy]# which pip /usr/bin/pip

[root@galaxy1 galaxy]# sh 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 Fetching https://pypi.python.org/packages/source/v/virtualenv/virtualenv-13.1.2.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 1679k 100 1679k 0 0 1565k 0 0:00:01 0:00:01 --:--:-- 1566k Verifying /tmp/galaxy-virtualenv-TFryjb/virtualenv-13.1.2.tar.gz checksum is aabc8ef18cddbd8a2a9c7f92bc43e2fea54b1147330d65db920ef3ce9812e3dc New python executable in .venv/bin/python Installing setuptools, pip, wheel...done. Activating virtualenv at .venv Collecting pip>=8.1 Using cached pip-8.1.2-py2.py3-none-any.whl Installing collected packages: pip Found existing installation: pip 7.1.2 Uninstalling pip-7.1.2: Successfully uninstalled pip-7.1.2 Successfully installed pip-8.1.2 Collecting bx-python==0.7.3 (from -r requirements.txt (line 2)) Could not fetch URL https://wheels.galaxyproject.org/simple/bx-python/: There was a problem confirming the ssl certificate: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:765) - skipping Could not find a version that satisfies the requirement bx-python==0.7.3 (from -r requirements.txt (line 2)) (from versions: ) No matching distribution found for bx-python==0.7.3 (from -r requirements.txt (line 2))

ADD COMMENTlink written 2.1 years ago by njoebott30
0
gravatar for irmny
2.1 years ago by
irmny0
irmny0 wrote:

Judging by your other question I assume you have beaten this particular problem. On my Centos 7 system I have the same problem except that I just bypass the problem by running:

sh run.sh --no-replace-pip

I know this is not a solution but it works for now. When I check my pip version it definitely says that it is the correct version.

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by irmny0

Thanks for the follow-up on this. I was able to move pass the original issue on CentOS 7; however, I ran into a myriad of other issues. So I went to Ubuntu and was able to get it running in short order using the above command option. Thanks again.

ADD REPLYlink written 2.1 years ago by njoebott30
0
gravatar for dcwest
2.1 years ago by
dcwest0
dcwest0 wrote:

I had a similar issue trying to install a local instance on my Mac. After lots of confusion and several tries getting the correct pip installed in the correct place, I simply tried downloading Python 2.7.11 instead of just 2.7 -- that seemed to resolve this issue for me!

ADD COMMENTlink written 2.1 years ago by dcwest0

Thanks for the reply. The python version that comes with CentOS7 is 2.7.5. I had upgraded it to the latest version - 2.7.11 but still ran into issues . Ubuntu 14.04 has python version 2.7.6 - and has worked well so far.

ADD REPLYlink written 2.1 years ago by njoebott30
0
gravatar for guillaume.lhostis
10 weeks ago by
guillaume.lhostis0 wrote:

On Mac OS X 10.13.5 got the similar error. I tried this (https://stackoverflow.com/questions/40485380/cant-upgrade-pip-to-the-newest-version-9-0-1-osubuntu-16-04lts?utm_medium=organic&utm_source=google_rich_qa&utm_campaign=google_rich_qa):

pip3 install -U pip

It worked after with sh run.sh.

ADD COMMENTlink written 10 weeks ago by guillaume.lhostis0
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