Question: 'Problem determining Galaxy's configuration'
2
gravatar for sf_17
8 months ago by
sf_1730
sf_1730 wrote:

I'm trying to install galaxy for local use. I have cloned the github repo and setup a conda environment running python 2.7. The first time I run

sh run.sh

galaxy starts up no problem and I can access it at localhost:8080

However, every time I try to start up after the first time I get the following error message:

Exception: Problem determining Galaxy's configuration - the specified configuration file cannot be found.

I tried copying over the config/galaxi.ini.sample file to config/galaxi.ini both before and after the first time I run run.sh. In both cases, galaxy starts up the first time I run it then gives me the same error message after.

Has anyone run into this issue before?

Thank you

galaxy • 215 views
ADD COMMENTlink modified 8 months ago by danielsauceda60 • written 8 months ago by sf_1730
1

Umm. 2 things

  1. please put more of the Log
  2. I suspect that you messed up the Conda configuration somewhere in you galaxy.ini. Can you post what you modified in galaxy.ini?
ADD REPLYlink written 8 months ago by danielsauceda60

Ah...that may be it. I haven't modified anything in the copied over galaxi.ini file (except for adding myself as an admin user and uncommenting that line). What should I be changing in galaxi.ini to play nice with my conda environment?

Here's more of the log

migrate.versioning.repository DEBUG 2017-08-18 13:52:25,050 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'GalaxyTools'), ('version_table', 'migrate_tools'), ('required_dbs', '[]')]))])

Traceback (most recent call last): File "/Users/student/Google Drive/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 58, in paste_app_factory app = galaxy.app.UniverseApplication( global_conf=global_conf, **kwargs )

File "/Users/student/Google Drive/galaxy/lib/galaxy/app.py", line 75, in __init__ self._configure_models( check_migrate_databases=True, check_migrate_tools=check_migrate_tools, config_file=config_file )

File "/Users/student/Google Drive/galaxy/lib/galaxy/config.py", line 1037, in _configure_models verify_tools( self, install_db_url, config_file, install_database_options )

File "/Users/student/Google Drive/galaxy/lib/tool_shed/galaxy_install/migrate/check.py", line 66, in verify_tools raise Exception( "Error attempting to update the value of migrate_tools.version: %s" % output )

Exception: Error attempting to update the value of migrate_tools.version: Traceback (most recent call last):

File "./scripts/manage_tools.py", line 15, in <module> config_file = read_config_file_arg( sys.argv, 'config/galaxy.ini', 'universe_wsgi.ini' )

File "/Users/student/Google Drive/galaxy/lib/galaxy/model/orm/scripts.py", line 49, in read_config_file_arg return find_config_file( default, old_default, config_file, cwd=cwd )

File "/Users/student/Google Drive/galaxy/lib/galaxy/util/properties.py", line 24, in find_config_file raise Exception("Problem determining Galaxy's configuration - the specified configuration file cannot be found.")

Exception: Problem determining Galaxy's configuration - the specified configuration file cannot be found.

ADD REPLYlink modified 8 months ago • written 8 months ago by sf_1730
1

I have not used conda myself but lets try some stuff.

First read this about conda. This would make sense why it works the first time and not after. Because it means that a .venv is getting created and breaking when conda is involved so --skip-venv flag like it says.

See what happens

ADD REPLYlink written 8 months ago by danielsauceda60
1

Ah that's a great find, thank you for the link. It looks like if I activate the conda environment before running sh run.sh, it should automatically run it with --skip-venv raised.

One thing I didn't think much about was that I cloned the galaxy repo into my Google Drive folder (named $HOME/Google Drive/). I didn't think twice about it, was just trying to have a cloud backup. But in the past I've had a few issues putting things in the google drive folder (sometimes it's as dumb as the default google drive directory name having a space in it). I moved it out of my drive directory into $HOME and it looks like it's starting up consistently now....super frustrating

Thank you for your help! This link to the admin doc page is really helpful

ADD REPLYlink written 8 months ago by sf_1730
1
gravatar for danielsauceda
8 months ago by
Texas A&M
danielsauceda60 wrote:

----------------------[solved]--------------------------

ADD COMMENTlink written 8 months ago by danielsauceda60
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