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.
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