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.fernandez@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-dev@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*
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/