In the documentation here: https://github.com/bgruening/docker-galaxy-stable#extending-the-docker-image--toc

It mentions RUN install-tools $GALAXY_ROOT/my_tool_list.yml with no reference to where install-tools comes from or how to use it.

In the redder bands of LSST, and presumably other cameras too, the best focus occurs when the geometric focus of the optics is located in the bulk of the silicon rather than at the surface.

I think simulating this can be achieved via a focus_depth kwarg to SiliconSensor and some small changes around https://github.com/GalSim-developers/GalSim/blob/releases/2.2/src/Silicon.cpp#L602. I guess

Sentry Issue: HB-GALAXY-VY

OSError: [WinError 123] The filename, directory name, or volume label syntax is incorrect: 'C:\\WINDOWS\\iun504.exe C:\\Program Files (x86)\\Blades of Avernum'

local\winappfinder.py in _find_executable at line 70
        location = uk.install_location_path \

wrapper for RNAz needs fixing

• Score [which] strand should be param type select:
  • forward
  • reverse
  • both
• use (di/mono)nucleotide shuffled z-scores should be select.
• mononucleotide shuffled z-scores may also be broken in source...not sure yet. When used on my set (~100) of (diverse) sequence al

Its clear that some of the conventions I've adopted for code and testing are unclear. For example:

• What is the different between an unmasked image, a 1D image and 2D image?

• Why does a tracer have images called blurred_profile_image_plane_images? How do these different from normal images? Model images?

• What does a 5x5 fixture mean?

Basically, the abstractions are good, but it need

The template for the supervisord.conf sets an invalid value in the [supervisorctl] section of the supervisord.conf.j2 template.

password = {SHA}{{ supervisor_password|hash('sha1') }}

The documentation for Supervisor config file format (http://supervisord.org/configuration.html#supervisorctl-section-settings) states that:

The password to pass to the supervisord server for use

Galaxy configuration default values should be for first time players. Now values are pretty much random and require modification each time.

in https://github.com/ARTbio/ansible-artimed/blob/master/docs/installing%20tools%20and%20workflows.md#installing-tools

the command to run to ultimately install tools and workflows is not indicated