Hello Sheldon,

What is the configuration setting you are using for the location to install 
repositories?  This is defined by the tool_path attribute of the <toolbox> tag 
in your shed_tools_conf.xml file.  The default is:

<toolbox tool_path="../shed_tools">

On Feb 28, 2014, at 3:47 PM, "Briand, Sheldon" <sheldon.bri...@ssc-spc.gc.ca> 

> Hi,
> No joy on the migration strategy.  Deseq is example of a tool that I 
> installed successfully yesterday.

Do you mean that you installed the deseq repository from the main tool shed:


and that its contained deseq tool "DE Seq (version 1.0.0)" was properly 
displayed in your Galaxy tool panel?  If so, what is now happening?

> Bowtie2 is an example of a tool that isn’t showing up even though the web 
> interface indicates that it is successfully installed.

Can you uninstall the repsository and reinstall it?  If so, what happens?

> Here is my directory structure relating to bowtie2:
> $ find . -name "*bowtie2*"
> ./shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2
> ./shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/package_bowtie2_2_1_0
> ./shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/package_bowtie2_2_1_0/017a00c265f1/package_bowtie2_2_1_0
> ./shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/ffa30bedbee3/tophat2/.hg/store/data/tool-data/bowtie2__indices.loc.sample.i
> ./shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/ffa30bedbee3/tophat2/tool-data/bowtie2_indices.loc.sample
> ./galaxy-dist/.hg/store/data/tool-data/bowtie2__indices.loc.sample.i
> ./galaxy-dist/.hg/store/data/tools/sr__mapping/bowtie2__wrapper.xml.i
> ./galaxy-dist/.hg/store/data/tools/sr__mapping/bowtie2__wrapper.py.i
> ./galaxy-dist/.hg/store/data/test-data/bowtie2
> ./galaxy-dist/tool-data/bowtie2_indices.loc.sample
> ./galaxy-dist/tool-data/bowtie2_indices.loc
> ./galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/ffa30bedbee3/bowtie2_indices.loc
> ./galaxy-dist/dependancies/samtools/0.1.18/devteam/bowtie2
> ./galaxy-dist/dependancies/samtools/0.1.19/iuc/package_samtools_0_1_19/00e17a794a2e/bin/bowtie2sam.pl
> ./galaxy-dist/dependancies/bowtie2
> ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/bowtie2
> ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0
> ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/bowtie2-align
> ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/bowtie2-build-debug
> ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/bowtie2-inspect-debug
> ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/bowtie2
> ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/bowtie2-inspect
> ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/bowtie2-align-debug
> ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/bowtie2-build
> [galaxy@eugene galaxy]$ cd 
> shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/
> I seem to be missing the .py and .xml files in the shed_tools directory.
> -Sheldon
> From: Briand, Sheldon 
> Sent: Friday, February 28, 2014 2:11 PM
> To: 'Greg Von Kuster'
> Subject: RE: [galaxy-dev] tool trouble
> Hi,
> Thanks for getting back to me.
> I didn’t get your first reply (email trouble here) when I sent my second 
> email.  I have not played with the sql tables.
> I think my problem is that I need to run tool migration scripts.  The 
> reinstall log I sent was for tophat 2.  It didn’t show up in 
> shed_tool_conf.xml after the update so I thought it had once again failed.  
> After I sent the email I noticed that tophat2 had shown up in the tool menu 
> (not where I wanted it but it was there).  So I looked around and there was 
> an entry in migrated_tools_conf.xml.
> I think the tools I am missing are because I likely missed the migration 
> step.  I’ll try that first and report back.
> Cheers,
> -Sheldon       
> From: Greg Von Kuster [mailto:g...@bx.psu.edu] 
> Sent: Friday, February 28, 2014 11:04 AM
> To: Briand, Sheldon
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] tool trouble
> Hello Briand,
> This may take some back-and-forth with you to understand the steps you have 
> taken so far.  Successfully installing a repository that contains tools 
> usually results in the tools being displayed in the Galaxy tool panel.  
> However, there may be issues that result in the tools not properly loading.  
> This often occurs when you stop and restart your Galaxy instance.  Your 
> Galaxy pasxter log will include information about any tool that does not 
> properly load.  Uninstalling and reinstalling the repository will usually not 
> have any affect on this.
> On Feb 28, 2014, at 9:17 AM, "Briand, Sheldon" <sheldon.bri...@ssc-spc.gc.ca> 
> wrote:
> Hi,
> I’ve been poking around a bit more. It looks as though galaxy isn’t actually 
> downloading and installing the tools.  The tool status changes to installed 
> in the web interface and postgres but the tool is not present on disk. 
> What is present on disk?  If you install a repository with tools, the 
> repository revision's contents should be on disk.  However, if the repository 
> is uninstalled, disk files are deleted.  Do you have repositories that are 
> installed but do not have any files on disk?
> The log below shows no download and make of the tool and dependancies.  
> Hopefully the log gives a bit more information.  Sorry for the second email.
> tool_shed.util.shed_util_common DEBUG 2014-02-28 09:58:48,567 Updating an 
> existing row for repository 'tophat2' in the tool_shed_repository table, 
> status set to 'New'.
> tool_shed.util.repository_dependency_util DEBUG 2014-02-28 09:58:48,714 
> Creating repository dependency objects...
> The log looks ok at first inspection, but it's not useful without more 
> information.
> From: galaxy-dev-boun...@lists.bx.psu.edu 
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, Sheldon
> Sent: Thursday, February 27, 2014 8:18 PM
> To: galaxy-dev@lists.bx.psu.edu
> Subject: [galaxy-dev] tool trouble
> Hi,
> I’m having trouble with some of my tools not appearing in the Analyze Data 
> menu.  I’ve successfully installed the tools via the manage installed tool 
> shed repositories(so they are installed to disk).  I have tried uninstalling 
> and installing again. 
> The above should not be necessary.  When you install, are you checking the 
> optional checkboxes to install repository dependencies and tool dependencies? 
>  If so, are they installing as well?
> The tool installs but does not appear in the menu. 
> Do you have an example of a repository that contains tools that installls 
> corruptly, but the tools do not load into the tool panel?
> Other tools install the menu updates just fine. 
> Do you have an example of a repsoitory that contains tools that do show up in 
> the tool panel after successfule repository installation?
> This is probably due to me corrupting the misbehaving tools installation 
> somehow.  I’m guessing that I need to uninstall the tool and wipe some 
> postgres entries.
> I strongly advise not manually changing inaything in your database suing sql 
> commands.  If you have done this, it could be the cause of the behavor you 
> are describing.  The Galaxy UI or API should be used.
> Greg Von Kuster
> My shed tool path:
> <toolbox tool_path="../shed_tools">
> My current version:
> parent: 12441:dc067a95261d
>  Added tag release_2014.02.10 for changeset 5e605ed6069f
> branch: stable
> Could someone point me in the right direction?
> Thanks,
> -Sheldon
> Sheldon Briand
> NRC Research Computing Support Analyst
> Research Computing Support / Soutien Informartique a la Recherche
> Operations, Science Portfolio / Operations, Portefeuil des sciences
> Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
> Halifax, NS  B3H 3Z1
> 902 426-1677
> sheldon.bri...@ssc-spc.gc.ca
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