I'd +1 to separating out workflows, if the tools are already available the
process shouldn't require an admin to install them (not when you can
download/upload manually). Should definitely have some separation
there...unfortunately all of my ideas consist of me putting aside other
work projects for a month to work on toolshed stuff. It's, likewise, no
secret that I desperately want to overhaul it.



2015-04-07 13:34 GMT-05:00 John Chilton <jmchil...@gmail.com>:

> Yes. Exactly.
>
> I created a few cards from some of your specific suggestions:
>
> https://trello.com/c/oC9iC4dx
> https://trello.com/c/j9RQxd6M
> https://trello.com/c/MFyTxcgq
>
> From my perspective - empowering users to find workflows however and
> request missing tools and giving deployers access to more easily
> install missing tools from the workflow screen would be bigger wins -
> but are perhaps a little more challenging.
>
> There is a lot that needs to be done to improve workflow importing
> generally and workflow importing from the Tool Shed specifically. I
> would call the current implementation something of a prototype - the
> deployer experience is confusing, the user experience is less than
> ideal, I am pretty sure Galaxy's concept of the workflows and their
> lineages and disconnected from the tool sheds - so things like updates
> haven't been thought through, etc....
>
> The problem is probably obvious - the ambitions of the tool shed and
> workflow subsystems are exceeded by the number of developer hours
> dedicated to them. Given that more people use tools than workflows in
> the tool shed and by wide margin - I think the current devteam focus
> on updating tools, improving the experience for tool developers,
> improving tool search, trying to fix tool testing, imporving
> dependency management, etc... makes sense. On the flip side of the
> coin - I have put a lot of effort into workflows but focused on
> expressiveness, etc... - again because I think those are more pressing
> problems right now than tool shed publication. I doesn't mean anyone
> thinks this isn't important - it is just we have to triage right?
>
> Three questions I have when thinking about workflows in the tool shed -
>
> 1) I don't think anyone would disagree that we need to spend more time
> on these things - but do you think we are missing allocating our time
> on other things related to the tool shed and workflows and should
> instead we be more focused on this use case - workflows coming from
> the tool shed?
>
> 2) Is there anything I or anyone else can do to encourage more outside
> development? It is no secret that my focus is generally on doing
> things that will encourage other developers to build awesome stuff.
> Any ideas how to create incentives for hacking on the tool shed.
>
> 3) Does putting workflows in the tool shed make sense fundamentally -
> if we do find time to invest a lot more work on this - should
> enhancing that process be the focus or should we find/build something
> more tailored to workflow distribution and optimized for user facing
> applications (the tool shed is meant to be deployer facing instead of
> user facing IMO).
>
> -John
>
>
> On Wed, Apr 1, 2015 at 9:56 AM, Peter Cock <p.j.a.c...@googlemail.com>
> wrote:
> > Hello all,
> >
> > I've been playing with the Tool Shed lately for publishing
> > Galaxy workflows - and realised the download process is
> > still very complicated, especially the final hurdle - importing
> > the workflow in order to actually use it.
> >
> > For the following example I am starting from a clean state -
> > an almost fresh Galaxy installation with NOTHING as yet
> > installed from the Tool Shed (see end of email), and I want
> > to install a single workflow:
> >
> > https://toolshed.g2.bx.psu.edu/view/peterjc/blast_top_hit_species
> >
> > 1. Goto Galaxy in browser, eg http://localhost/galaxy-dev/
> > 2. Goto "User", "Register"
> > 3. Create account using address added to admin_users
> > earlier in config/galaxy.ini
> > 4. Click "Return to the home page"
> > 5. Since logged in as admin, can goto "Admin" settings
> > 6. Select "Search and browse tool sheds"
> > 7. Select "Galaxy Main Tool Shed"
> > 8. Enter "species" in the search box
> > 9. Select "blast_top_hit_species"
> > 10. Note the list of dependencies
> > 11. Click "Install into Galaxy"
> > 12. Leave the dependency handling ticked.
> > 13. Ponder that the section selection will apply to? The current
> > repository has no tools but some of the dependencies do...
> > I don't want to bundle the BLAST tools in the same section as
> > the text manipulation tools. Go with the default (don't pick a section).
> > 14. Click "install"
> > 15. Wait as the following are installed:
> >
> > Name Description Owner Revision
> > blast_top_hit_species Workflow to count species of top nr BLASTX hits
> > of a transcriptome peterjc db0c1bb92308
> > ncbi_blast_plus NCBI BLAST+ devteam 2fe07f50a41e
> > blast_datatypes BlastXml and other blast datatypes devteam 5482a8cd0f36
> > package_blast_plus_2_2_29 NCBI BLAST+ 2.2.29 (binaries only) iuc
> a2ec897aac2c
> > package_biopython_1_65 Downloads and compiles version 1.65 of the
> > Biopython package. biopython dc595937617c
> > package_numpy_1_9 Contains a tool dependency definition that downloads
> > and compiles version 1.9 of the the python numpy package. iuc
> > 84e97f5cd3ab
> > package_atlas_3_10 Contains a tool dependency definition that
> > downloads and compiles version 3.10 of the the Automatically Tuned
> > Linear Algebra Software. iuc 37ff27ea37ed
> > fasta_to_tabular FASTA-to-Tabular converter devteam 9d189d08f2ad
> > sample_seqs Sub-sample sequences files (e.g. to reduce coverage)
> > peterjc 02c13ef1a669
> > unique Advanced unique lines program using GNU sort bgruening
> 7ce75adb93be
> >
> > 16. Get bored, especially if the page appears to have stalled.
> > Try reloading the page which goes back to the "Admin" welcome.
> > Now how do I get back to the installation status...
> > 17. Click on "Manage installed tool shed repositories"
> > 18. If at this point some of the dependency requirements are in
> > error state, try a round of repairing repositories (and watch at
> > the terminal, e.g. compiling numpy is slow).
> > 19. Admire all the nice green "tick" icons and "Installed" entries.
> > 20. Notice the tiny grey "cog" icon against the workflow
> > repository, "blast_top_hit_species".
> > 21. Read the legend, "This repository contains exported workflows",
> > which is encouraging but there is nothing on the page hinting at
> > *how* to actually use the new workflow.
> > 22. Try the context menu to see if that lets you use the workflow. No.
> > 23. At this point I fully explored the workflow menus looking for an
> > import option, and gave up and returned to "Manage installed tool
> > shed repositories".
> > 23. Ignore the context menu, click on "blast_top_hit_species".
> > 24. Click on the top right "repository actions" menu
> > 25. Find nothing about importing a workflow.
> > 26. Click on the "Species of top BLAST hits" entry under
> > "Contents of this repository"
> > 27. Observe pretty SVG image of workflow.
> > 24. Click on the top right "repository actions" menu
> > 25. Notice the menu now offers "import workflow to galaxy".
> > 26. Click on "import workflow to galaxy".
> > 26. Back at SVG with green message "Workflow Species of top
> > BLAST hits imported successfully. "
> > 27. Return to "Analyze Data" (or "Workflows") and finally the
> > workflow is available (although probably only for the Galaxy
> > administrator's personal account).
> > 28. Cry because all the new tools are dumped in the top level
> > tool menu (see step 13).
> >
> > Possible suggestions to make this easier:
> >
> > At step 21, include a clue in the legend?
> >
> > At step 22 and 25, include "Import all these workflows" in menu?
> >
> > At step 24, change the button to "repository/workflow actions"
> > since it includes some actions specific to the viewed workflow?
> >
> > How about the common use case where the Galaxy Admin
> > was asked to import the workflow for a specific user? Can
> > we have an action "Import workflow for specific user"?
> >
> > Also I think the tool section behaviour for dependencies needs
> > clarification (step 13/28). From a tool author perspective, I would
> > like to be able to set the default section for each tool (see also
> > past requests to set the order they are added to the tool panel).
> >
> > Regards,
> >
> > Peter
> >
> > --
> >
> >
> > This was how I setup my current galaxy development instance
> > tracking the default dev branch on github:
> >
> > $ cd ~/repositories
> > $ git clone https://github.com/galaxyproject/galaxy.git
> > $ cd galaxy
> >
> > I made minor config changes, including adding myself as
> > an admin user via the admin_users setting:
> >
> > $ emacs config/galaxy.ini
> > ...
> >
> > I also setup Apache to serve this instance at
> > http://localhost/galaxy-dev/ and set ToolShed path to be
> > ~/repositories/shed_tools/
> >
> > This was working fine. To hopefully reset this back to a what
> > is almost a clean slate (for this bug report), I next removed
> > the auto-generated XML files, data files and SQLite database,
> > and tool shed files:
> >
> > $ rm -f ~/repositories/galaxy/*.xml
> > $ rm -f ~/repositories/galaxy/config/*.xml
> > $ rm -f ~/repositories/galaxy/database/universe.sqlite
> > $ rm -rf ~/repositories/galaxy/database/files/*
> > $ rm -rf ~/repositories/shed_tools/
> >
> > (Dangerous - which is why I explicitly used the full paths!)
> >
> > I then restart Galaxy,
> >
> > $ cd ~/repositories/galaxy
> > $ ./run.sh
> > ...
> >
> > Note it creates a new empty SQLite database etc.
> > ___________________________________________________________
> > Please keep all replies on the list by using "reply all"
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> >
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> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
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>



-- 
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048
e...@tamu.edu
rasche.e...@yandex.ru
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