Hernan,
Sorry for the slow response here, have you made any progress? I'd be glad to help sort this out.
Instead of creating an alias to a particular python in your .bashrc, I'd recommend that if you're having problems you should manually create the virtualenv with the specific python version you want. Once you've done that, on galaxy's first start, it'll populate the requirements correctly.
An example command would be:
virtualenv -p /usr/local/bin/python2.7 .venv
Execute this command from the galaxy directory, and it'll create a virtualenv named .venv, which is what Galaxy expects to use. After that, just start Galaxy and the requirements should be installed to .venv automatically.
-Dannon
On Wed, Nov 9, 2016 at 2:39 PM, Hernán Piqueras yjmrs@hotmail.com wrote:
I have a Linux with both Python 2.6 and Python 2.7. Apparently Python is so bad designed that you cannot simply upgrade from 2.6 to 2.7 without breaking your system. As latest Galaxy works with Python 2.7, I put an alias in my .bashrc to /usr/local/bin/python2.7 and the same with virtualenv. I also enabled bash debugging and enabled expanded alias into .sh scripts.
Then I ran :
$ sh galaxy/run.sh
... lots of output ---
Requirement already satisfied: pysam==0.8.4+gx1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.7.0.dev5->-r requirements.txt (line 51)) ++ PYTHONPATH=lib ++ /usr/local/bin/python2.7 -c 'import galaxy.dependencies; print '''\n'''.join(galaxy.dependencies.optional('''config/galaxy.ini'''))' Traceback (most recent call last): File "<string>", line 1, in <module> File "/home/galaxy/galaxy/lib/galaxy/dependencies/__init__.py", line 9, in <module> from galaxy.util import asbool File "/home/galaxy/galaxy/lib/galaxy/util/__init__.py", line 31, in
<module> from six import binary_type, iteritems, PY3, string_types, text_type ImportError: No module named six + GALAXY_CONDITIONAL_DEPENDENCIES= + exit 1
If I check with root user, six package is installed. My guess was I am missing an alias to pip2.7, then I added such alias in my .bashrc and again:
$ sh galaxy/run.sh
... lots of output ---
++ '[' -n /bin/bash -o -n '' ']' ++ hash -r
- unset PYTHONPATH
- '[' -z /home/galaxy/galaxy/.venv ']'
- : https://wheels.galaxyproject.org/simple
- '[' 1 -eq 1 ']'
- /usr/local/bin/pip2.7 install 'pip>=8.1'
Traceback (most recent call last): File "/usr/local/bin/pip2.7", line 5, in <module> from pkg_resources import load_entry_point File "/usr/local/lib/python2.7/site-packages/distribute-0.6. 44-py2.7.egg/pkg_resources.py", line 2850, in <module> working_set.require(__requires__) File "/usr/local/lib/python2.7/site-packages/distribute-0.6. 44-py2.7.egg/pkg_resources.py", line 696, in require needed = self.resolve(parse_requirements(requirements)) File "/usr/local/lib/python2.7/site-packages/distribute-0.6. 44-py2.7.egg/pkg_resources.py", line 594, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: pip==9.0.1
# pip --version pip 9.0.1 from /usr/local/lib/python2.7/site-packages/pip-9.0.1-py2.7.egg (python 2.7) I have installed Python 2.7 and its tools (virtualenv, pip, etc) following official guidelines.
How can install the missing dependecies?
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