figure out how to leverage existing work

[martenson]

we have

https://github.com/jegalle/CustomGalaxyFlavors by @jegalle https://github.com/wookoouk/galaxyFlavorGenerator by @wookoouk running at http://wookoouk.github.io/galaxyFlavorGenerator/

[bgruening]

I haven't heart from @jegalle. I suppose he is very busy.

[doomedramen]

I need to talk to you @martenson before I can continue, hangouts|Skype?

On Wed, 5 Aug 2015, 16:04 Martin Cech notifications@github.com wrote:

we have

https://github.com/jegalle/CustomGalaxyFlavors by @jegalle https://github.com/jegalle https://github.com/wookoouk/galaxyFlavorGenerator by @wookoouk https://github.com/wookoouk running at http://wookoouk.github.io/galaxyFlavorGenerator/

— Reply to this email directly or view it on GitHub https://github.com/galaxyFlavorsGenerators/galaxyFlavorGenerator/issues/6 .

[martenson]

@wookoouk I prefer async but if you want we can do a teleconference

[doomedramen]

just wanted a text chat to clear up some issues with the tool shed api, we should talk on here so its documented

[martenson]

as of today the Main Tool Shed has all the repos and tools indexed and available for searching at /api/repositories and /api/tools

[doomedramen]

Thats great news, Ill add that now

[doomedramen]

can /api/repositories be queried for a specific tool id?

[martenson]

@wookoouk nope, what would be the usecase?

[doomedramen]

queried the tool api, now want to display the github info for that tool, would assume i would need to then query the repo api to get the info per tool

[martenson]

Should be addressed with https://github.com/galaxyFlavorsGenerators/galaxyFlavorGenerator/issues/7 If the need arises we can extend the toolsearch API to include more information.

[doomedramen]

That would be awesome :D

On Wed, 5 Aug 2015 at 19:16 Martin Cech notifications@github.com wrote:

Should be addressed with #7 https://github.com/galaxyFlavorsGenerators/galaxyFlavorGenerator/issues/7 If the need arises we can extend the toolsearch API to include more information.

— Reply to this email directly or view it on GitHub https://github.com/galaxyFlavorsGenerators/galaxyFlavorGenerator/issues/6#issuecomment-128095971 .

[doomedramen]

hmm, the repo name is not what I expected:

name:kraken_filter repo_owner_name: cschu repo_name: kraken_tools

name:kraken_combine repo_owner_name: cschu repo_name: kraken_tools

I do not have the unique info for using the install-repository tool as the current output is: RUN install-repository \ "--url https://toolshed.g2.bx.psu.edu/ -o cschu --name kraken_tools" \ "--url https://toolshed.g2.bx.psu.edu/ -o cschu --name kraken_tools" \ "--url https://toolshed.g2.bx.psu.edu/ -o devteam --name kraken_translate" \ "--url https://toolshed.g2.bx.psu.edu/ -o devteam --name kraken" \ "--url https://toolshed.g2.bx.psu.edu/ -o devteam --name kraken_report" \ "--url https://toolshed.g2.bx.psu.edu/ -o devteam --name kraken_report" \

[doomedramen]

example from search for 'kraken' all 3 tools have the same repo_owner_username and repo_name

format: name : repo_owner_username : repo_name

Kraken-translate : devteam : tool-data Kraken-filter : devteam : tool-data Kraken-mpa-report : devteam : tool-data

[doomedramen]

is repo_name incorrect? @bgruening pointed out that for Kraken-filter the repo_name should be 'kraken_filter' (not 'tool-data')

[bgruening]

@martenson repo_name is not exposed correctly. The name is the tool-name or tool-id and the repo_name does not make sense to me.

[doomedramen]

Just checked, this is only an issue on MAIN TS, Its fine on TEST TS

[bgruening]

Ha! Great, all what we need is an TS update! :)

[doomedramen]

forcing it to use TEST TS fixes the issue:

"--url https://testtoolshed.g2.bx.psu.edu/ -o cschu --name kraken_tools" \ 
"--url https://testtoolshed.g2.bx.psu.edu/ -o devteam --name kraken_translate" \ 
"--url https://testtoolshed.g2.bx.psu.edu/ -o devteam --name kraken" \ 
"--url https://testtoolshed.g2.bx.psu.edu/ -o devteam --name kraken_filter" \ 
"--url https://testtoolshed.g2.bx.psu.edu/ -o devteam --name kraken_report" \ 

[martenson]

there was older index on test (not broken yet) - thats why it worked

[doomedramen]

Searching for 'data_manager' returns different things on MAIN and TEST

MAIN: [{ "times_downloaded": 707, "last_updated": "less than a month", "name": "data_manager", "approved": "no", "id": "2b6bab33b168bf9f", "homepage_url": null, "full_last_updated": "2015-07-08 05:07 PM", "repo_owner_username": "devteam", "long_description": "", "remote_repository_url": null, "description": "Builds sam indexes using the new data table format." }, { "times_downloaded": 122, "last_updated": "less than a month", "name": "data_manager", "approved": "no", "id": "5316e9b4eb9a4965", "homepage_url": null, "full_last_updated": "2015-07-09 11:03 PM", "repo_owner_username": "iuc", "long_description": "Manage GEMINI databases. This tools will retrieve all files for the use in GEMINI.\r\n\r\nRepository-Maintainer: Björn Grüning\r\nRepository-Development: https://github.com/galaxy-iuc/tool_shed/", "remote_repository_url": null, "description": "Manage GEMINI annotation data" }, { "times_downloaded": 74, "last_updated": "less than a month", "name": "data_manager", "approved": "no", "id": "1a540b81b0eb54a1", "homepage_url": null, "full_last_updated": "2015-07-15 11:05 PM", "repo_owner_username": "bgruening", "long_description": "", "remote_repository_url": null, "description": "Diamond data manager" }]

The name does not seem correct

TEST

[{ "times_downloaded": 205, "last_updated": "less than a year", "name": "data_manager", "approved": "no", "id": "acb3dc7f802404ed", "homepage_url": null, "full_last_updated": "2015-06-30 08:30 PM", "repo_owner_username": "blankenberg", "long_description": "data_manager_fetch_genome_all_fasta", "remote_repository_url": null, "description": "data_manager_fetch_genome_all_fasta" }, { "times_downloaded": 55, "last_updated": "less than a month", "name": "data_manager", "approved": "no", "id": "160434ce3ad1f16a", "homepage_url": null, "full_last_updated": "2015-07-14 03:01 AM", "repo_owner_username": "devteam", "long_description": "data_manager_gatk_picard_index_builder", "remote_repository_url": null, "description": "data_manager_gatk_picard_index_builder" }, { "times_downloaded": 61, "last_updated": "less than a month", "name": "data_manager", "approved": "no", "id": "911ca76da76707d7", "homepage_url": null, "full_last_updated": "2015-07-22 07:52 PM", "repo_owner_username": "jjohnson", "long_description": "faToTwoBit builds a 2bit index of a nucleic fasta file that can be used with blat and gfServer", "remote_repository_url": null, "description": "data_manager_ucsc_twobit_index_builder" }]

the name still appears to be wrong, the description and long_description seem to be the correct name

[martenson]

MTS and TTS have different non-synchronized content - they are bound to give you different results.

The name will be fixed after https://github.com/galaxyproject/galaxy/pull/566 is merged and deployed.

[doomedramen]

awesome, thanks name is the bit holding me back at the moment.

@martenson @bgruening which tool shed should I use for the flavor generator for now? TEST?

[martenson]

MTS, but give me 15mins to propagate the changes and rebuild the index

On Thu, Aug 6, 2015 at 11:19 AM Martin Page notifications@github.com wrote:

awesome, thanks name is the bit holding me back at the moment.

@martenson https://github.com/martenson @bgruening https://github.com/bgruening which tool shed should I use for the flavor generator for now? TEST?

— Reply to this email directly or view it on GitHub https://github.com/galaxyFlavorsGenerators/galaxyFlavorGenerator/issues/6#issuecomment-128408538 .

[doomedramen]

Cool, that output was from repo search BTW, tool search is no longer being used for now

On Thu, 6 Aug 2015, 16:22 Martin Cech notifications@github.com wrote:

MTS, but give me 15mins to propagate the changes and rebuild the index

On Thu, Aug 6, 2015 at 11:19 AM Martin Page notifications@github.com wrote:

awesome, thanks name is the bit holding me back at the moment.

@martenson https://github.com/martenson @bgruening https://github.com/bgruening which tool shed should I use for the flavor generator for now? TEST?

— Reply to this email directly or view it on GitHub < https://github.com/galaxyFlavorsGenerators/galaxyFlavorGenerator/issues/6#issuecomment-128408538

.

— Reply to this email directly or view it on GitHub https://github.com/galaxyFlavorsGenerators/galaxyFlavorGenerator/issues/6#issuecomment-128409356 .

[martenson]

https://testtoolshed.g2.bx.psu.edu/api/repositories?q=kraken https://testtoolshed.g2.bx.psu.edu/api/tools?q=kraken

proceeding with MTS

[doomedramen]

Great news, thanks for the quick turn around on this

[martenson]

MTS updated and regenerated, going for lunch

[doomedramen]

Looks good my end, now testing

[doomedramen]

Now leaving work for the day, push a demo of where I am up to: http://wookoouk.github.io/galaxyFlavorGenerator/

[bgruening]

Awesome, will test and report back!

[doomedramen]

The docker building many be broken...

On Thu, 6 Aug 2015, 17:19 Björn Grüning notifications@github.com wrote:

Awesome, will test and report back!

— Reply to this email directly or view it on GitHub https://github.com/galaxyFlavorsGenerators/galaxyFlavorGenerator/issues/6#issuecomment-128425028 .

[doomedramen]

The changes are: Guthub links where available. Moved from tool search to repo search. Tooltips with description. Better (still buggy) dockerfiles. Started biojs registry search.

On Thu, 6 Aug 2015, 17:26 Martin Page wookoouk@gmail.com wrote:

The docker building many be broken...

On Thu, 6 Aug 2015, 17:19 Björn Grüning notifications@github.com wrote:

Awesome, will test and report back!

— Reply to this email directly or view it on GitHub https://github.com/galaxyFlavorsGenerators/galaxyFlavorGenerator/issues/6#issuecomment-128425028 .

[bgruening]

This rocks! And the generated Dockerfile looks also good. A few minor things I have seen so far! Many thanks @wookoouk

• [x] GALAXY_CONFIG_BRAND should be configurable
• [ ] The user should be able to choose the Galaxy release
• [ ] maybe a choosen repository should disappear from the search-box?
• [ ] if you change the search term from gemini to vcf really quick the search will not be triggered
• [x] The search spinner looks a lot like a windows logo, can we just default to the Galaxy one?
• [x] "Your Galaxy will have the following:" should only appear if you have an item
• [x] "Repo" should be renamed to "Source Code"?
• [ ] Linking to the TS would be nice

[doomedramen]

All that should be pretty easy to implement. Will do it tomorrow

On Thu, 6 Aug 2015, 17:32 Björn Grüning notifications@github.com wrote:

This rocks! And the generated Dockerfile looks also good. A few minor things I have seen so far! Many thanks @wookoouk https://github.com/wookoouk

• GALAXY_CONFIG_BRAND should be configurable
• The user should be able to choose the Galaxy release
• maybe a choosen repository should disappear from the search-box?
• if you change the search term from gemini to vcf really quick the search will not be triggered
• The search spinner looks a lot like a windows logo, can we just default to the Galaxy one?
• "Your Galaxy will have the following:" should only appear if you have an item
• "Repo" should be renamed to "Source Code"?
• Linking to the TS would be nice

— Reply to this email directly or view it on GitHub https://github.com/galaxyFlavorsGenerators/galaxyFlavorGenerator/issues/6#issuecomment-128428521 .

[martenson]

Awesome work.

Using repo search is fine but tool search has its uses. My ideal take would be to incorporate both (maybe using tabs). And when the tool is selected you would query the repo (or I extend the API to provide all info needed) and add it.

[doomedramen]

I could have its search both and tag the results as to if they are tools or repos.

On Thu, 6 Aug 2015, 17:46 Martin Cech notifications@github.com wrote:

Awesome work. Using repo search is fine but tool search has its uses. My ideal take would be to incorporate both (maybe using tabs).

— Reply to this email directly or view it on GitHub https://github.com/galaxyFlavorsGenerators/galaxyFlavorGenerator/issues/6#issuecomment-128436863 .

[martenson]

I feel they need distinct lists as the search score is not comparable and it would probably create ordering confusion and ux problem.

[doomedramen]

Okay, I'll have a crack at it :)

On Thu, 6 Aug 2015, 17:52 Martin Cech notifications@github.com wrote:

I feel they need distinct lists as the search score is not comparable and it would probably create ordering confusion and ux problem.

— Reply to this email directly or view it on GitHub https://github.com/galaxyFlavorsGenerators/galaxyFlavorGenerator/issues/6#issuecomment-128438997 .

[martenson]

@wookoouk Those are just ideas, implement what you want obviously. :)

Btw would you like to transfer your repo under this organization? And what is your thinking regarding licence?

[doomedramen]

More than happy to move to Org. I normally go for MIT.

On Thu, 6 Aug 2015, 18:04 Martin Cech notifications@github.com wrote:

@wookoouk https://github.com/wookoouk Those are just ideas, implement what you want obviously. :)

Btw would you like to transfer your repo under this organization? And what is your thinking regarding licence?

— Reply to this email directly or view it on GitHub https://github.com/galaxyFlavorsGenerators/galaxyFlavorGenerator/issues/6#issuecomment-128444946 .

[doomedramen]

Updated your checklist (above)

[jegalle]

Hi

I just got back from holidays, maybe i should have told you guys.

Had some time to mess around in reactjs and added a 'base image select' where the user is able to select one of @bgruening 's flavors. I've already sent a pull request to @wookoouk .

Hope it helps!

[martenson]

@jegalle awesomeness!

[doomedramen]

@jegalle :+1:

[bgruening]

@jegalle welcome back!

[bgruening]

I will close this and create a new one with the checklist.