I assume you have a proper entry for the deseq_and_sam2count repository in your shed_tool_conf.xml file (please confirm).  What does the relevant section of your Galaxy paster log show when attempts are made to load the tools contained in this repository at server startup?

On Feb 28, 2014, at 4:02 PM, "Briand, Sheldon" <Sheldon.Briand@SSC-SPC.gc.ca> wrote:

Hi,
 
Yep thatís what I have.
 
Here is deseq:
find . -name "*deseq*"
./galaxy-dist/dependancies/R_3_0_1/3.0.1/iuc/package_deseq2_1_0_17
./galaxy-dist/dependancies/deseq2
./galaxy-dist/dependancies/deseq2/1.0.17/iuc/package_deseq2_1_0_17
./galaxy-dist/dependancies/deseq2/1.0.17/iuc/package_deseq2_1_0_17/0e80b1827773/deseq2
 
-Sheldon
 
From: Greg Von Kuster [mailto:greg@bx.psu.edu] 
Sent: Friday, February 28, 2014 4:59 PM
To: Briand, Sheldon
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] tool trouble
 
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.Briand@SSC-SPC.gc.ca> wrote:


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 isnít 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
./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/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 didnít 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 didnít 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.  Iíll try that first and report back.
 
Cheers,
-Sheldon       
 
From: Greg Von Kuster [mailto:greg@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.Briand@ssc-spc.gc.ca> wrote:

 

Hi,
 
Iíve been poking around a bit more. It looks as though galaxy isnít 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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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,
 
Iím having trouble with some of my tools not appearing in the Analyze Data menu.  Iíve 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.  Iím 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
SSC-NRC / SPC-CNRC
Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
Halifax, NS  B3H 3Z1
902 426-1677
 
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