What is "niceName" in:

• https://bitbucket.org/lorainelab/integrated-genome-browser/src/master/galaxy/bedgraph.xml
  Why is it necessary to replace spaces with underscore characters?

Galaxy:

• https://github.com/galaxyproject/galaxy

Suggestion: stand up your own Galaxy to test and develop external viewer XML

Instructions:

• https://galaxyproject.org/admin/get-galaxy/

Looks like files in this "shared" directory map genome assembly database keys maintained in Galaxy and external viewer names for same:
https://github.com/galaxyproject/galaxy/tree/dev/tool-data/shared
May be able to reference column headings as variable names in the external viewer XML

Steps to set up Galaxy on local (my Mac):

1. install virtualenv: pip install virtualenv
2. create virtual environment with python2: virtualenv --python=python2.7 galaxy
3. activate virtual environment: source galaxy/bin/activate
4. Check it's the right python:

(galaxy) local aloraine$ python
Python 2.7.10 (default, Oct 6 2017, 22:29:07)
[GCC 4.2.1 Compatible Apple LLVM 9.0.0 (clang-900.0.31)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

Start Galaxy (inside cloned project)
$ sh run.sh

Error:

installing: requests-2.18.4-py36h4516966_1 ...
installing: conda-4.3.31-py36_0 ...
installation finished.
galaxy.tools.deps.conda_util DEBUG 2019-05-30 17:17:36,906 Executing command: /Users/aloraine/galaxy/database/dependencies/_conda/bin/conda install -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults conda=4.3.33
Fetching package metadata .................
Solving package specifications: .

Package plan for installation in environment /Users/aloraine/galaxy/database/dependencies/_conda:

The following packages will be UPDATED:

conda: 4.3.31-py36_0 --> 4.3.33-py36_0 conda-forge

conda-4.3.33-p 100% |################################| Time: 0:00:00 6.16 MB/s
executing: .venv/bin/uwsgi --module 'galaxy.webapps.galaxy.buildapp:uwsgi_app()' --virtualenv /Users/aloraine/galaxy/.venv --pythonpath lib --threads 4 --buffer-size 16384 --http localhost:8080 --static-map /static/style=/Users/aloraine/galaxy/static/style/blue --static-map /static=/Users/aloraine/galaxy/static --die-on-term --hook-master-start 'unix_signal:2 gracefully_kill_them_all' --hook-master-start 'unix_signal:15 gracefully_kill_them_all' --enable-threads --py-call-osafterfork
Traceback (most recent call last):
File ".venv/bin/uwsgi", line 6, in <module>
from uwsgi import run
ImportError: dlopen(/Users/aloraine/galaxy/.venv/lib/python2.7/site-packages/uwsgi.so, 2): Library not loaded: /usr/local/opt/pcre/lib/libpcre.1.dylib
Referenced from: /Users/aloraine/galaxy/.venv/lib/python2.7/site-packages/uwsgi.so
Reason: image not found
(galaxy) local aloraine$

repeated, same error.

Works. I opened a new Terminal and tried to execute run.sh. This time, everything downloaded and Galaxy started up.

I have reviewed the .xml files in the IGB project and in https://github.com/galaxyproject/galaxy/blob/dev/display_applications/igb
The files in the Galaxy repository are the most up-to-date.
I am removing the galaxy directory in the IGB project.

Removed galaxy directory. Project builds and tests successfully finish without this. Changes are on branch:
https://bitbucket.org/aloraine/alorainefork/branch/IGBF-1759

Merged to master.