Hi Edgar,

it’s a good idea to use python2.7 for galaxy, since 16.01 is the last
release supporting python 2.6.
In general you can create a new virrtualenv with a a specific python
interpreter like this:

virtualenv -p <path/to/python/interpreter> <path/to/new/virtualenv/>

If you create a new new virtualenv .venv in your galaxy source folder,
run.sh will pick this up.
If you are using a different way to start galaxy, you can use something
along the lines of

<path/to/virtualenv/bin/python <path/to/galaxy>/scripts/paster.py
serve <path/to/galaxy/>config/galaxy.ini>

Hope that will get you past the problems starting up galaxy.

Cheers,
Marius
​

On 19 May 2016 at 14:48, Fernandez Edgar <edgar.fernan...@umontreal.ca>
wrote:

> Hey Guys,
>
>
>
> I’ve fixed my first problem with the environment.
>
> But I’m still getting the second one.
>
>
>
> Also, did any of you guys try to deploy galaxy with Microsoft Azure?
>
> I’m actually looking into it and I was wondering if you had any input…
>
>
>
> Let me know if you have any info on my libchtslib.so: input error or
> Microsoft Azure.
>
>
>
> Cheers!
>
>
>
> *Edgar Fernandez*
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la Communication
>
> *Université de Montréal*
>
>
>
> PAVILLON ROGER-GAUDRY, bureau X-210
>
> (  Bur. : *1-514-343-6111 poste 16568*
>
>
>
>
>
> *From:* Fernandez Edgar
> *Sent:* May-18-16 2:00 PM
> *To:* galaxy-...@bx.psu.edu
> *Subject:* RE: [galaxy-dev] not sure what I can do about this...
>
>
>
> Hey Guys,
>
>
>
> Hope everyone is doing well.
>
>
>
> So I’m back at galaxy v16.01
>
>
>
> I’m having a small problem.
>
> My python system version is 2.6.6
>
>
>
> So I installed python version 2.7.8 from  Software Collection Library
> release 1.2 packages for Oracle Linux 6 (x86_64)
> <https://ulns.dit.umontreal.ca/rhn/channels/ChannelDetail.do?cid=149>
>
> This means I need to source an environment before being about to use it.
>
> So what I’ve created a file config/local_env.sh with:
>
> *# Source python27*
>
> *export PATH=/opt/rh/python27/root/usr/bin${PATH:+:${PATH}}*
>
> *export
> LD_LIBRARY_PATH=/opt/rh/python27/root/usr/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}*
>
> *export MANPATH=/opt/rh/python27/root/usr/share/man:${MANPATH}*
>
> *# For systemtap*
>
> *export
> XDG_DATA_DIRS=/opt/rh/python27/root/usr/share${XDG_DATA_DIRS:+:${XDG_DATA_DIRS}}*
>
> *# For pkg-config*
>
> *export
> PKG_CONFIG_PATH=/opt/rh/python27/root/usr/lib64/pkgconfig${PKG_CONFIG_PATH:+:${PKG_CONFIG_PATH}}*
>
>
>
> These export comes directly with the installation of python 2.7.8 in the
> file /opt/rh/python27/enable.
>
> But when I started my galaxy it didn’t stick.
>
>
>
> I had to insert those exports into the file run.sh right before the
> following line:
>
> *./scripts/common_startup.sh $common_startup_args || exit 1*
>
>
>
> Any suggestions to make it work?
>
>
>
> Also, I get this error :
>
> *Traceback (most recent call last):*
>
> *  File "./scripts/paster.py", line 27, in <module>*
>
> *    serve.run()*
>
> *  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py",
> line 1061, in run*
>
> *    invoke(command, command_name, options, args[1:])*
>
> *  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py",
> line 1067, in invoke*
>
> *    exit_code = runner.run(args)*
>
> *  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py",
> line 223, in run*
>
> *    result = self.command()*
>
> *  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py",
> line 639, in command*
>
> *    app = loadapp( app_spec, name=app_name, relative_to=base,
> global_conf=vars)*
>
> *  File
> "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line
> 295, in loadapp*
>
> *    return loadobj(APP, uri, name=name, **kw)*
>
> *  File
> "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line
> 319, in loadobj*
>
> *    global_conf=global_conf)*
>
> *  File
> "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line
> 344, in loadcontext*
>
> *    global_conf=global_conf)*
>
> *  File
> "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line
> 368, in _loadconfig*
>
> *    return loader.get_context(object_type, name, global_conf)*
>
> *  File
> "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line
> 506, in get_context*
>
> *    section)*
>
> *  File
> "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line
> 565, in _context_from_explicit*
>
> *    value = import_string(found_expr)*
>
> *  File
> "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line
> 125, in import_string*
>
> *    return pkg_resources.EntryPoint.parse("x=" + s).load(False)*
>
> *  File
> "/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pkg_resources.py",
> line 2260, in load*
>
> *    entry = __import__(self.module_name, globals(),globals(),
> ['__name__'])*
>
> *  File "/home/galaxy/galaxy-v16.01/lib/galaxy/web/buildapp.py", line 5,
> in <module>*
>
> *    from galaxy.webapps.galaxy.buildapp import app_factory*
>
> *  File
> "/home/galaxy/galaxy-v16.01/lib/galaxy/webapps/galaxy/buildapp.py", line
> 15, in <module>*
>
> *    import galaxy.app*
>
> *  File "/home/galaxy/galaxy-v16.01/lib/galaxy/app.py", line 6, in
> <module>*
>
> *    from galaxy import config, jobs*
>
> *  File "/home/galaxy/galaxy-v16.01/lib/galaxy/jobs/__init__.py", line 19,
> in <module>*
>
> *    from galaxy import model, util*
>
> *  File "/home/galaxy/galaxy-v16.01/lib/galaxy/model/__init__.py", line
> 26, in <module>*
>
> *    import galaxy.datatypes.registry*
>
> *  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/registry.py",
> line 9, in <module>*
>
> *    import tabular*
>
> *  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/tabular.py", line
> 18, in <module>*
>
> *    from galaxy.datatypes.sniff import get_headers*
>
> *  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/sniff.py", line
> 19, in <module>*
>
> *    from galaxy.datatypes.binary import Binary*
>
> *  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/binary.py", line
> 13, in <module>*
>
> *    import pysam*
>
> *  File
> "/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/__init__.py",
> line 1, in <module>*
>
> *    from pysam.libchtslib import **
>
> *ImportError:
> /home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so:
> undefined symbol: gzopen64*
>
> *Removing PID file paster.pid*
>
>
>
> PLEASE HELP ME !
>
>
>
> Best regards,
>
>
>
> *Edgar Fernandez*
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la Communication
>
> *Université de Montréal*
>
>
>
> PAVILLON ROGER-GAUDRY, bureau X-210
>
> (  Bur. : *1-514-343-6111 poste 16568*
>
> ___________________________________________________________
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