Re: [galaxy-dev] not sure what I can do about this...

19 May 2016

      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