Machine Polish (hopefully pre-GCC 2016)

[jmchilton]

Ordered by importance (by Martin)

Should have

Nice to have

• link to the galaxy log on the desktop of the virtual machine. (https://github.com/galaxyproject/planemo-machine/blob/master/roles/galaxyprojectdotorg.devbox/tasks/main.yml)
• Turn off Terminal scrollback limits. (https://github.com/galaxyproject/planemo-machine/blob/master/roles/galaxyprojectdotorg.devbox/tasks/main.yml)
• Turn off Terminal scroll on update. (https://github.com/galaxyproject/planemo-machine/blob/master/roles/galaxyprojectdotorg.devbox/tasks/main.yml)
• change font size for terminal (https://github.com/galaxyproject/planemo-machine/blob/master/roles/galaxyprojectdotorg.devbox/tasks/main.yml)
• Do you have to restart galaxy to see the tool? Hot load? (This is a bug - those tools should definitely show up.)
• missing creation of a tool_dependencies.xml file which would be required for the seqkt and bwa tools to actually work if downloaded from the toolshed (place in planemo maybe?)
• disable screen saver
• Nginx should not say "forbidden" while starting up - it should say "Galaxy is unavailable - it may be starting..." (https://github.com/galaxyproject/ansible-galaxy-extras/blob/master/templates/nginx.conf.j2)
• change prompt (maybe just cwd, rather than default whole path ubuntu uses) (https://github.com/galaxyproject/planemo-machine/blob/master/roles/galaxyprojectdotorg.devbox/tasks/main.yml)
• enable IEs in default config (https://github.com/galaxyproject/planemo-machine/blob/master/group_vars/all#L115)
• ensure docker images for IEs are pulled (maybe... -John)
• npm install proxy stuff (This is probably done by ansible-galaxy-extras now? https://github.com/galaxyproject/ansible-galaxy-extras/blob/master/defaults/main.yml#L158 - might have to witch defaults to enable it)
• Install bioblend-tutorial and place link on Desktop - https://github.com/nsoranzo/bioblend-tutorial (https://github.com/galaxyproject/planemo-machine/blob/master/roles/galaxyprojectdotorg.devbox/tasks/main.yml)

Already Has

• 🔥 🔥 rebuild the image with the latest addition of komodo
• Atom does not start Atom editor does not start up for me.  #73
• remove link to Atom from the desktop (since it is not used anymore) (should be fixed by add desktop link for komodo; drop atom and its mentions #81)
• 🔥 fix miniconda on the .ova image ova image: conda does not have write access #78
• 🔥 add link to komodo-edit to the desktop (should be fixed by add desktop link for komodo; drop atom and its mentions #81)
• problem with tool_init in appliance tutorial (appliance tutorial: problem with planemo tool_init #74)
• provide TS bootstrapping in virt appliance (virtual appliance: correct bootstrapping the TS #76)
• set of default keyboards (Add the keyboard layout switcher to the panel. #70?) (en_US, en_GB, de)
• less default cpus and more vram reduce number of requested procs, add more vram #72
• Document clipboard use in documentation. (https://github.com/galaxyproject/planemo/tree/master/docs)
• Devbox role should apt-get update before completion to eliminate warnings about new packages. (https://github.com/galaxyproject/planemo-machine/blob/master/roles/galaxyprojectdotorg.devbox/tasks/main.yml)
• Xubuntu profile should turn new package warning off altogether also. (WIP: updates all over  #62) (https://github.com/galaxyproject/planemo-machine/blob/master/roles/galaxyprojectdotorg.devbox/tasks/main.yml)
• provide a $GALAXY_ROOT (or $GALAXY) , so we can use that in docs and it'll work. E.g "Please cd to $GALAXY/lib/web/proxy/..." (Add the keyboard layout switcher to the panel. #70) (https://github.com/galaxyproject/planemo-machine/blob/master/roles/galaxyprojectdotorg.devbox/tasks/main.yml)
• Move OVA docs first in appliance list. (https://github.com/galaxyproject/planemo/tree/master/docs)
• Upgrade planemo (I think this would be covered with continuous building and testing).
• Install google chrome. (WIP: updates all over  #62) (https://github.com/galaxyproject/planemo-machine/blob/master/roles/galaxyprojectdotorg.devbox/tasks/main.yml)

[martenson]

Added feedback from galaxyproject/planemo#241 (comment) via @Christian-B
Also removed the bug label. Muhehe.

[nsoranzo]

I'd also add: consolidate the 2 images (GCC2015-i386.ova and planemo) into 1.

[hexylena]

@martenson it's totally a bug :P

[hexylena]

@nsoranzo definitely

[davebx]

I'll be working my way through the list of issues per @jmchilton's request.

[jmchilton]

@davebx A million thanks - beer debt plus 4 or 5 - I'll go through and a little implementation note to some those then to at least point where I'd start looking at those if it were me.

[davebx]

Awesome, @jmchilton. All help gaining context is appreciated.

[bgruening]

@davebx I started to work on this as well. Here are my recent updates: https://github.com/galaxyproject/planemo-machine/compare/updates?expand=1

[martenson]

maybe disable screen saver?

[martenson]

the .ova image has the folllowing problems:

• video memory is set to 8MB which makes the rendering of the UI troublesome, especially when trying to work fullscreen - more reasonable default would be 32MB
• number of processors is set to 4 (which gives warning unless you have 4 physical processors on host)- I changed it to 1 and have no problems

[nsoranzo]

@martenson: +1, I had the same issues

[martenson]

cpus and vram should be addressed by #72

[martenson]

I modified the first comment and reordered it, I think we need to polish a bit more and we don't have much time.

[martenson]

the tool_init and TS bootstrapping are resolved, however Atom still does not start and Conda does not have write permissions in: /opt/miniconda (#78)

ping @jmchilton @davebx

[jmchilton]

I like the emoji - thanks!

Is there a workaround at runtime for the atom problem? Does it work from the CLI?

[martenson]

@jmchilton I was not able to start atom in any way. When I installed miniconda manually it works fine so there is that. We really need an editor though, I tried installing sublime-text from the unofficial apt-get repo but that is also broken. gedit?

[jmchilton]

@martenson This worked before 😦.

Can you try sudo apt-get install xubuntu-desktop and see if that re-enables it?

If not, sudo apt-get install kate?

My guess is that https://github.com/galaxyproject/planemo-machine/pull/69/files broke this.

[martenson]

@jmchilton on it, will take a while since @Comcast sucks

[martenson]

@jmchilton sudo apt-get install xubuntu-desktop does not help Atom (It might need to be present during installation? However when I uninstall and install it again it behaves the same 💩)

kate installs and works fine...

[martenson]

komodo-edit also works and I consider it superior to kate

sudo add-apt-repository ppa:mystic-mirage/komodo-edit
sudo apt-get update
sudo apt-get install komodo-edit

[martenson]

I am rebuilding the machine to test komodo installation now

[jmchilton]

Thanks for testing - that looks like a great option.

[martenson]

@jmchilton ha, can't build shit cos can't install packer cos can't install mercurial cos curl: (6) Could not resolve host: mercurial.selenic.com 😆

[martenson]

Well I overcame that but hit another problem: Homebrew/homebrew-core#2325

In the meantime I am building the machine on my machine.

[jmchilton]

I am going to close this out now - and I have opened a new issue for 2017 #85 . Hopefully the image holds up tomorrow. I really appreciate all the effort that went into making the 2016 image - a huge thanks to @martenson, @bgruening, and @davebx!