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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