Hello Björn,

Thanks very much for your message!  Please see my inline comments.


On Apr 2, 2013, at 4:33 PM, Björn Grüning wrote:

> I have tested a few things regarding to the toolshed and prepared a
> complex module-dependency-beast, with meta-package and
> orhphan-tool-dependencies and so on. A few problems I encountered are
> summarized below. You can try it by yourself, if you install the
> chemicaltoolbox package from the testtoolshed.
> 
> - three crashes with traceback attached, during tool-installation
> 
> - one 'name' not defined error, with attached patch


Thanks very much for finding this issue and for the patch.  We've applied it in 
changeset 9252:da2d6ee29f30 in our stable branch, so it is running on both 
public Galaxy tool sheds.


> 
> - For me the the installation of tools with really complex and long
> compiling steps are stalled in 'Installing' forever. Try to install the
> osra package (it often hangs, but not every time). 
> Its not possible to uninstall/reinstall these dependencies
> without touching the database. And the error says, tool is already
> installed. Would be nice if the admin is able to reset that repository
> easily, even if it is limbo ... (is there a timeout somewhere?)
> Error: paste.httpserver.ThreadPool WARNING 2013-04-02 22:02:41,256 Thread 
> 140246687659776 hung (working on task for 1964 seconds)
> (The SystemExit: traceback attached)

I've create the following Trello card for this issue:

https://trello.com/card/toolshed-enable-galaxy-admin-to-reset-tool-dependencies-when-timeout-occurs/506338ce32ae458f6d15e4b3/761

There are 4 places where this timeout may be occurring: Galaxy tool shed 
server, Galaxy tool shed nginx, a proxy server at your end, or your local 
Galaxy server.  There is not enough information in your attached traceback log 
to determine where the timeout is occurring.  Can you provide me your Galaxy 
server's IP address so I can look in logs at our end?


> 
> - It would be great if the tool-developer or the admin has more control
> over the location of the tools in the toolbar. Installing meta package
> leaves you with only one choice, regardless how many tools are bundled. 


Support for this will be available in the next Galaxy release.  There are 
Trello cards for this here:

https://trello.com/card/toolshed-enhance-the-current-galaxy-api-for-installing-repositories-from-the-tool-shed/506338ce32ae458f6d15e4b3/734
https://trello.com/card/toolshed-add-features-that-leverage-the-galaxy-api-for-installing-repositories-from-the-tool-shed/506338ce32ae458f6d15e4b3/735


> 
> - Installing dependencies will leave me with empty folders under
> galaxy-root with the name of the dependency. My guess is, 
> that if I manually download a file/folder with wget, the folder is not 
> purged, but the content is.


Our intent is that installing repositories from the tool shed is completely 
automated with no manual intervention required.  Tool dependency definitions 
should not use utilities like wget to download dependencies because these 
utilities may not be available in the environments (e.g. vanilla mac os) into 
which the repositories are being installed.  I'll enhance the tool dependency 
tag sets as necessary to accommodate additional download and install 
requirements.  Can you let me know if the current download_by_url needs 
enhancements?


> 
> - Often after upgrading the tool_dependencies.xml file, I was not able
> to 'get updates' from the toolshed. The version was up-to-data, but it
> wasn't. Deinstalling and Installing fixed it. But I think its ab bug,
> isn't it?

This very well may be a bug.  Can you please provide additional details so that 
I can reproduce this behavior?  I'll get a fix asap.


> 
> - Is there a way, to just download a python file, not zipped and add it to 
> PYTHONPATH?
> If I download it with <action type="download_by_url"> I have problems to copy 
> that file with move.
> I would like to download it with wget, but one download by URL is required. 
> My current solution is, 
> to include a dummy download_by_url and than fetch with wget, or download a 
> archive version.

I've created the following Trello card for this issue:

https://trello.com/card/toolshed-enhance-the-download-by-url-process-for-installing-tool-dependencies/506338ce32ae458f6d15e4b3/760


> 
> - Is it correct that a repository referenced only in
> tool_dependencies.xml is not enough to install? numpy was only
> referenced as tool_dependency and I got the error that the tool (with
> owner and revision) was not found. After adding to repository_dependency
> it was ok.

Can you provide more details about your question above (e.g., the 
tool_dependencies.xml fie would help).  I want to make sure i understand the 
issue.  

Thanks very much Björn,

Greg Von Kuster




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