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))
