Hi Greg,

Also for bowtie2.  I can confirm that it doesn't have an entry in the 
shed_tool_conf.xml file.  Sorry I didn't mention these before.  Its been a long 
week and there obviously was a problem between my chair and keyboard.  :)

-Sheldon


________________________________________
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] 
On Behalf Of Briand, Sheldon [sheldon.bri...@ssc-spc.gc.ca]
Sent: Friday, February 28, 2014 6:02 PM
To: 'Greg Von Kuster'
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] tool trouble

Hi,

So those are the ones that work.

One of the ones that doesn’t work is bowtie2:
tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 
16:03:14,476 Adding an entry for revision 017a00c265f1 of repository 
package_bowtie2_2_1_0 owned by devteam to 
repository_dependencies_of_installed_repositories.
tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 
16:03:14,490 Adding an entry for revision 017a00c265f1 of reposito
ry package_bowtie2_2_1_0 owned by devteam to 
installed_repository_dependencies_of_installed_repositories.
tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 
16:03:14,502 Adding an entry for revision 017a00c265f1 of reposito
ry package_bowtie2_2_1_0 owned by devteam to 
tool_dependencies_of_installed_repositories.
tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 
16:03:14,516 Adding an entry for revision 017a00c265f1 of reposito
ry package_bowtie2_2_1_0 owned by devteam to 
installed_tool_dependencies_of_installed_repositories.
tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 
16:03:45,046 Adding an entry for version 2.1.0 of package bowtie2
to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
galaxy.tools.data DEBUG 2014-02-28 16:04:39,615 Loaded tool data table 
'bowtie2_indexes'

No tool ID loaded (loaded from the .xml file in the shed_tools dir?).  And no 
file .xml fileor .py file in the shed_tools directory.  But a successful 
install in the admin interface.

I appreciate you looking into this for me.

-Sheldon

From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Friday, February 28, 2014 5:51 PM
To: Briand, Sheldon
Subject: Re: [galaxy-dev] tool trouble

Hi Sheldon,

I'm not sure what to advise you to do here as all of the information looks ok.  
It's not clear at all why the tools are not displayed in your tool panel.  Are 
they loaded but simply hidden (set to not be visible)?  Did you make any 
changes to your integrated_tool_panel.xml file?  If not, try deleting it an 
restartign your Galaxy server (the file gets automatically recreated if 
missing).  I can't think of anything else to take a look at on this.  Sorry I'm 
not able to be very helpful here.

On Feb 28, 2014, at 4:24 PM, "Briand, Sheldon" 
<sheldon.bri...@ssc-spc.gc.ca<mailto:sheldon.bri...@ssc-spc.gc.ca>> wrote:


Hi,

Yes for deseq and sam2count:

<section id="ngs:rnaseq" name="NGS:RNAseq" version="">
  <tool 
file="toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/deseq/deseq.xml<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/deseq/deseq.xml>"
 guid="too
lshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/deseq/1.0.0<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/deseq/1.0.0>">
      <tool_shed>toolshed.g2.bx.psu.edu<http://bx.psu.edu></tool_shed>
        <repository_name>deseq_and_sam2counts</repository_name>
        <repository_owner>nikhil-joshi</repository_owner>
        
<installed_changeset_revision>a49aff09553e</installed_changeset_revision>
        
<id>toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/deseq/1.0.0<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/deseq/1.0.0></id>
        <version>1.0.0</version>
    </tool>
    <tool 
file="toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/deseq/sam2counts.xml<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/deseq/sam2counts.xml>"
 gu
id="toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/sam2counts/1.0.0<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/sam2counts/1.0.0>">
      <tool_shed>toolshed.g2.bx.psu.edu<http://bx.psu.edu></tool_shed>
        <repository_name>deseq_and_sam2counts</repository_name>
        <repository_owner>nikhil-joshi</repository_owner>
        
<installed_changeset_revision>a49aff09553e</installed_changeset_revision>
        
<id>toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/sam2counts/1.0.0<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/sam2counts/1.0.0></id>
        <version>1.0.0</version>
    </tool>
</section>

galaxy.tools DEBUG 2014-02-28 16:10:18,298 Loaded tool id: 
toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/deseq/1.0.0<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/deseq/1.0.0>,
 ve
rsion: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-02-28 16:10:18,310 Loaded tool id: 
toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/sam2counts/1.0<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/sam2counts/1.0>.
0, version: 1.0.0 into tool panel.

-Sheldon

From: Greg Von Kuster [mailto:g...@bx.psu.edu<http://bx.psu.edu>]
Sent: Friday, February 28, 2014 5:19 PM
To: Briand, Sheldon
Cc: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] tool trouble

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.bri...@ssc-spc.gc.ca<mailto:sheldon.bri...@ssc-spc.gc.ca>> wrote:



Hi,

Yep that’s what I have.

Here is deseq:
find . -name "*deseq*"
./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts>
./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts>
./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/.hg/store/data/deseq<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/.hg/store/data/deseq>
./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/.hg/store/data/deseq/deseq._r.sample.i<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/.hg/store/data/deseq/deseq._r.sample.i>
./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/.hg/store/data/deseq/deseq.xml.i<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/.hg/store/data/deseq/deseq.xml.i>
./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/.hg/store/data/deseq/deseq<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/.hg/store/data/deseq/deseq>
./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/.hg/store/data/deseq/deseq/deseq.xml.i<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/.hg/store/data/deseq/deseq/deseq.xml.i>
./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/.hg/store/data/deseq/deseq/deseq._r.i<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/.hg/store/data/deseq/deseq/deseq._r.i>
./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/.hg/store/data/deseq/deseq._r.i<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/.hg/store/data/deseq/deseq._r.i>
./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/deseq<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/deseq>
./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/deseq/deseq.R<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/deseq/deseq.R>
./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/deseq/deseq.xml<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/deseq/deseq.xml>
./shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/package_deseq2_1_0_17<http://bx.psu.edu/repos/iuc/package_deseq2_1_0_17>
./shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/package_deseq2_1_0_17/0e80b1827773/package_deseq2_1_0_17<http://bx.psu.edu/repos/iuc/package_deseq2_1_0_17/0e80b1827773/package_deseq2_1_0_17>
./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:g...@bx.psu.edu<http://bx.psu.edu>]
Sent: Friday, February 28, 2014 4:59 PM
To: Briand, Sheldon
Cc: galaxy-dev@lists.bx.psu.edu<mailto: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.bri...@ssc-spc.gc.ca<mailto:sheldon.bri...@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:

http://toolshed.g2.bx.psu.edu/view/nikhil-joshi/deseq_and_sam2counts

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<http://bx.psu.edu/repos/devteam/bowtie2>
./shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/package_bowtie2_2_1_0<http://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<http://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<http://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<http://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<http://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/<http://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<mailto: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<mailto: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> 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu<mailto: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<mailto: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
SSC-NRC / SPC-CNRC
Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
Halifax, NS  B3H 3Z1
902 426-1677
sheldon.bri...@ssc-spc.gc.ca<mailto:sheldon.bri...@ssc-spc.gc.ca>

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