Known issues when installing LAPPS/Galaxy

This page has some known issues when installing a LAPPS/Galaxy instance as well as the workarounds. The following issues are discussed:

psycopg2

There are some problems with glibc on later versions of Ubuntu that may manifest as an error like:

ibresolv-2-c4c53def.5.so: symbol __res_maybe_init version GLIBC_PRIVATE not defined in file libc.so.6 with link time reference

The solution is to uninstall psycopg2 and re-install the binary only. It is probably wise to run this in Galaxy’s .venv.

$> source .venv/bin/activate
$> sudo pip uninstall psycopg2
$> pip install psycopg2-binary
$> deactivate

Logging error: logging.getLogger does not exist

In some cases on startup you get an error that a logging method is not available. This happens when you have the following configuration in the galaxy code:

lib/galaxy/util/submodules.py
lib/galaxy/util/logging/

The submodules script uses the Python logging module but because of the logging directory it cannot find it. There is nothing of value in the logging directory and it is there only because at some point you installed an instance from another branch of the galaxy code.

Solution: remove the logging directory.

Missing migration scripts

You may see the following error:

AssertionError: There is no script for 136 version

This error occurs in /Applications/ADDED/galaxy/galaxy/lib/galaxy/model/migrate/check.py. Like the previous case, this can happen when you have switched between several branches or commits and a previous version leaves some pyc files. The check.py script runs a bunch of migrate scripts that update the database and it gets confused when there are pyc files that do not have a corresponding pyfile.

Migrate scripts are in /lib/galaxy/model/migrate/versions. In one case this directory had pyc and py script for all migration scripts up to number 135, but it also included

0136_collection_and_workflow_state.pyc
0137_add_copied_from_job_id_column.pyc
0138_add_hda_version.pyc
0139_add_history_dataset_association_history_table.pyc
0140_add_dataset_version_to_job_to_input_dataset_association_table.pyc
0141_add_oidc_tables.pyc
0142_change_numeric_metric_precision.pyc

Solution: remove those pyc files.

Updating the tool menu

The tool menu is changed by editing GalaxyMods/config/tool_conf.xml. When you do this on a running instance (at least with a local install) then refreshing the screen in your browser will actually give you a new menu. However, this does not work for all changes. For example, if you move a section of tools then nothing happens. This is because when you start an instance Galaxy will create a file named integrated_tool_panel.xml in the root directory. This file is used by the running instance to create the menu (after a refresh) and changing tool_conf.xml will change it. For example, tools in a section will be removed. But what will not change is the list of top-level sections and the order of them, only tool elements of those sections will be added, changed or removed.

This is not a problem when you remove an entire section in tool_conf.xml, it will still be in integrated_tool_panel.xml, but it will be empty and won’t be displayed.

Solution. If you need to change the order of the sections you have to remove integrated_tool_panel.xml and restart the instance.