tool trouble

classic Classic list List threaded Threaded
11 messages Options
| Threaded
Open this post in threaded view
|

tool trouble

Briand, Sheldon

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 tool installs but does not appear in the menu.  Other tools install the menu updates just fine.  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.

 

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

[hidden email]

 


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: tool trouble

Briand, Sheldon

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.  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.

 

Thanks,

-Sheldon

 

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...

tool_shed.util.shed_util_common DEBUG 2014-02-28 09:58:49,255 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 09:58:49,269 Building repository dependency relationships...

127.0.0.1 - - [28/Feb/2014:09:58:48 -0300] "POST /admin_toolshed/reinstall_repository?id=827fffb0dffdf266 HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/reselect_tool_pa

nel_section?sort=name&advanced_search=true&f-deleted=True&async=false&show_item_checkboxes=false&id=827fffb0dffdf266&page=1" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/201

00101 Firefox/24.0"

132.246.247.143 - - [28/Feb/2014:09:58:51 -0300] "GET /api/histories/c24fc4d33a334292/contents HTTP/1.0" 200 - "http://eugene.imb.nrc.ca/" "Mozilla/5.0 (X11; Linux x86_64; rv:2

4.0) Gecko/20100101 Firefox/24.0"

132.246.244.216 - - [28/Feb/2014:09:58:52 -0300] "GET /api/histories/289a2a0291e69024/contents HTTP/1.0" 200 - "http://eugene.imb.nrc.ca/root/index" "Mozilla/4.0 (compatible; M

SIE 7.0; Windows NT 6.1; WOW64; Trident/5.0; SLCC2; .NET CLR 2.0.50727; .NET CLR 3.5.30729; .NET CLR 3.0.30729; Media Center PC 6.0; .NET4.0C; .NET4.0E)"

galaxy.tools.data WARNING 2014-02-28 09:58:52,416 Cannot find index file './database/tmp/tmp-toolshed-gmfcr_q5JBB/bowtie2_indices.loc' for tool data table 'tophat2_indexes'

galaxy.tools.data DEBUG 2014-02-28 09:58:52,416 Loading another instance of data table 'tophat2_indexes', attempting to merge content.

127.0.0.1 - - [28/Feb/2014:09:58:52 -0300] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/reinstall_reposito

ry?id=827fffb0dffdf266" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0"

galaxy.tools.data DEBUG 2014-02-28 09:58:52,611 Loading another instance of data table 'tophat2_indexes', attempting to merge content.

galaxy.tools.test INFO 2014-02-28 09:58:52,624 tophat2 - Failed to find case matching value (No) for test parameter specification for conditional readGroup. Remainder of test b

ehavior is unspecified.

galaxy.tools.test INFO 2014-02-28 09:58:52,636 tophat2 - Failed to find case matching value (No) for test parameter specification for conditional readGroup. Remainder of test b

ehavior is unspecified.

galaxy.tools.test INFO 2014-02-28 09:58:52,650 tophat2 - Failed to find case matching value (No) for test parameter specification for conditional readGroup. Remainder of test b

ehavior is unspecified.

galaxy.tools.test INFO 2014-02-28 09:58:52,664 tophat2 - Failed to find case matching value (No) for test parameter specification for conditional readGroup. Remainder of test b

ehavior is unspecified.

galaxy.tools.data DEBUG 2014-02-28 09:58:53,154 Could not parse existing tool data table config, assume no existing elements: [Errno 2] No such file or directory: u'/software/p

ackages/galaxy/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/ffa30bedbee3/tool_data_table_conf.xml'

galaxy.tools.data DEBUG 2014-02-28 09:58:53,167 Loading another instance of data table 'tophat2_indexes', attempting to merge content.

galaxy.tools DEBUG 2014-02-28 09:58:53,516 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.6, version: 0.6 into tool panel.

127.0.0.1 - - [28/Feb/2014:09:58:55 -0300] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/reinstall_reposito

ry?id=827fffb0dffdf266" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0"

tool_shed.util.common_install_util DEBUG 2014-02-28 09:58:57,748 Attempting to install tool dependency package bowtie2 version 2.1.0.

tool_shed.util.tool_dependency_util DEBUG 2014-02-28 09:58:58,038 Updating an existing record for version 2.1.0 of tool dependency bowtie2 for revision ffa30bedbee3 of reposito

ry tophat2 by updating the status from Uninstalled to Never installed.

[localhost] local: touch ./dependancies/bowtie2/2.1.0/devteam/tophat2/ffa30bedbee3/env.sh

[localhost] local: echo 'if [ -f /software/packages/galaxy/galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/env.sh ] ; then . /software/package

s/galaxy/galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/env.sh ; fi' >> ./dependancies/bowtie2/2.1.0/devteam/tophat2/ffa30bedbee3/env.sh

tool_shed.util.common_install_util DEBUG 2014-02-28 09:58:58,216 Attempting to install tool dependency package samtools version 0.1.18.

tool_shed.util.tool_dependency_util DEBUG 2014-02-28 09:58:58,256 Updating an existing record for version 0.1.18 of tool dependency samtools for revision ffa30bedbee3 of reposi

tory tophat2 by updating the status from Uninstalled to Never installed.

[localhost] local: touch ./dependancies/samtools/0.1.18/devteam/tophat2/ffa30bedbee3/env.sh

[localhost] local: echo 'if [ -f /software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.18/devteam/package_samtools_0_1_18/171cd8bc208d/env.sh ] ; then . /software/pac

kages/galaxy/galaxy-dist/dependancies/samtools/0.1.18/devteam/package_samtools_0_1_18/171cd8bc208d/env.sh ; fi' >> ./dependancies/samtools/0.1.18/devteam/tophat2/ffa30bedbee3/e

nv.sh

tool_shed.util.common_install_util DEBUG 2014-02-28 09:58:58,438 Attempting to install tool dependency package tophat2 version 2.0.9.

tool_shed.util.tool_dependency_util DEBUG 2014-02-28 09:58:58,473 Updating an existing record for version 2.0.9 of tool dependency tophat2 for revision ffa30bedbee3 of reposito

ry tophat2 by updating the status from Uninstalled to Never installed.

[localhost] local: touch ./dependancies/tophat2/2.0.9/devteam/tophat2/ffa30bedbee3/env.sh

[localhost] local: echo 'if [ -f /software/packages/galaxy/galaxy-dist/dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473/env.sh ] ; then . /software/package

s/galaxy/galaxy-dist/dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473/env.sh ; fi' >> ./dependancies/tophat2/2.0.9/devteam/tophat2/ffa30bedbee3/env.sh

tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:58:58,687 Adding an entry for revision ffa30bedbee3 of repository tophat2 owned by devteam to reposito

ry_dependencies_of_installed_repositories.

tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:58:58,728 Adding an entry for revision ffa30bedbee3 of repository tophat2 owned by devteam to installe

d_repository_dependencies_of_installed_repositories.

127.0.0.1 - - [28/Feb/2014:09:58:58 -0300] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/reinstall_reposito

ry?id=827fffb0dffdf266" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0"

tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:58:58,751 Appending revision ffa30bedbee3 of repository tophat2 owned by devteam to all dependent repo

sitories in installed_dependent_repositories_of_installed_repositories.

tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:58:58,763 Adding an entry for revision ffa30bedbee3 of repository tophat2 owned by devteam to tool_dep

endencies_of_installed_repositories.

tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:58:58,789 Adding an entry for revision ffa30bedbee3 of repository tophat2 owned by devteam to installe

d_tool_dependencies_of_installed_repositories.

tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:58:58,800 Adding an entry for version 2.1.0 of package bowtie2 to runtime_tool_dependencies_of_install

ed_tool_dependencies.

tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:58:59,501 Adding an entry for version 2.1.0 of package bowtie2 to installed_runtime_dependent_tool_dep

endencies_of_installed_tool_dependencies.

tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:59:00,300 Adding an entry for version 0.1.18 of package samtools to runtime_tool_dependencies_of_insta

lled_tool_dependencies.

tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:59:01,006 Adding an entry for version 0.1.18 of package samtools to installed_runtime_dependent_tool_d

ependencies_of_installed_tool_dependencies.

tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:59:01,679 Adding an entry for version 2.0.9 of package tophat2 to runtime_tool_dependencies_of_install

ed_tool_dependencies.

tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:59:02,617 Adding an entry for version 2.0.9 of package tophat2 to installed_runtime_dependent_tool_dep

endencies_of_installed_tool_dependencies.

127.0.0.1 - - [28/Feb/2014:09:58:49 -0300] "POST /admin_toolshed/manage_repositories HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/reinstall_repository?id=827fffb0dffdf

266" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0"

127.0.0.1 - - [28/Feb/2014:09:59:03 -0300] "GET /admin_toolshed/monitor_repository_installation?tool_shed_repository_ids=827fffb0dffdf266 HTTP/1.1" 200 - "http://localhost:8080

/admin_toolshed/reinstall_repository?id=827fffb0dffdf266" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0"

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Briand, Sheldon
Sent: Thursday, February 27, 2014 8:18 PM
To: [hidden email]
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 tool installs but does not appear in the menu.  Other tools install the menu updates just fine.  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.

 

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

[hidden email]

 


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: tool trouble

Greg Von Kuster
<base href="x-msg://145/">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" <[hidden email]> 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: [hidden email] [mailto:galaxy-[hidden email]] On Behalf Of Briand, Sheldon
Sent: Thursday, February 27, 2014 8:18 PM
To: [hidden email]
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
 
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: tool trouble

Briand, Sheldon
<base href="x-msg://145/">

Hi,

 

No joy on the migration strategy.  Deseq is example of a tool that I installed successfully yesterday.  Bowtie2 is an example of a tool that isn’t showing up even though the web interface indicates that it is successfully installed.

 

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 [[hidden email]]
Sent: Friday, February 28, 2014 11:04 AM
To: Briand, Sheldon
Cc: [hidden email]
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" <[hidden email]> 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: [hidden email] [mailto:galaxy-[hidden email]] On Behalf Of Briand, Sheldon
Sent: Thursday, February 27, 2014 8:18 PM
To: [hidden email]
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

 

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

 


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: tool trouble

Greg Von Kuster
<base href="x-msg://145/">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" <[hidden email]> 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 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
./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 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 [[hidden email]] 
Sent: Friday, February 28, 2014 11:04 AM
To: Briand, Sheldon
Cc: [hidden email]
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" <[hidden email]> 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: [hidden email] [mailto:galaxy-[hidden email]] On Behalf Of Briand, Sheldon
Sent: Thursday, February 27, 2014 8:18 PM
To: [hidden email]
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
 
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/



___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: tool trouble

Briand, Sheldon
<base href="x-msg://145/">

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

./shed_tools/toolshed.g2.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

./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

./shed_tools/toolshed.g2.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

./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

./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

./shed_tools/toolshed.g2.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

./shed_tools/toolshed.g2.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

./shed_tools/toolshed.g2.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

./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:[hidden email]]
Sent: Friday, February 28, 2014 4:59 PM
To: Briand, Sheldon
Cc: [hidden email]
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" <[hidden email]> 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 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

./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 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 [[hidden email]] 
Sent: Friday, February 28, 2014 11:04 AM
To: Briand, Sheldon
Cc: [hidden email]
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" <[hidden email]> 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: [hidden email] [mailto:galaxy-[hidden email]] On Behalf Of Briand, Sheldon
Sent: Thursday, February 27, 2014 8:18 PM
To: [hidden email]
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

 

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

 


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: tool trouble

Greg Von Kuster
<base href="x-msg://145/">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" <[hidden email]> wrote:

Hi,
 
Yep that’s 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: [hidden email]
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" <[hidden email]> 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 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
./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 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 [[hidden email]] 
Sent: Friday, February 28, 2014 11:04 AM
To: Briand, Sheldon
Cc: [hidden email]
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" <[hidden email]> 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: [hidden email] [mailto:galaxy-[hidden email]] On Behalf Of Briand, Sheldon
Sent: Thursday, February 27, 2014 8:18 PM
To: [hidden email]
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
 
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/



___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: tool trouble

Briand, Sheldon
<base href="x-msg://145/">

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:[hidden email]]
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" <[hidden email]> wrote:



Hi,

 

Yes for deseq and sam2count:

 

<section id="ngs:rnaseq" name="NGS:RNAseq" version="">

      <tool_shed>toolshed.g2.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>

        <version>1.0.0</version>

    </tool>

      <tool_shed>toolshed.g2.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>

        <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, 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.

0, version: 1.0.0 into tool panel.

 

-Sheldon

 

From: Greg Von Kuster [mailto:greg@bx.psu.edu] 
Sent: Friday, February 28, 2014 5:19 PM
To: Briand, Sheldon
Cc: [hidden email]
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" <[hidden email]> wrote:




Hi,

 

Yep that’s 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: [hidden email]
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" <[hidden email]> 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 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

./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 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 [[hidden email]] 
Sent: Friday, February 28, 2014 11:04 AM
To: Briand, Sheldon
Cc: [hidden email]
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" <[hidden email]> 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: [hidden email] [mailto:galaxy-[hidden email]] On Behalf Of Briand, Sheldon
Sent: Thursday, February 27, 2014 8:18 PM
To: [hidden email]
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

 

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

 


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: tool trouble

Briand, Sheldon
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: [hidden email] [[hidden email]] On Behalf Of Briand, Sheldon [[hidden email]]
Sent: Friday, February 28, 2014 6:02 PM
To: 'Greg Von Kuster'
Cc: [hidden email]
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:[hidden email]]
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" <[hidden email]<mailto:[hidden email]>> 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:[hidden email]<http://bx.psu.edu>]
Sent: Friday, February 28, 2014 5:19 PM
To: Briand, Sheldon
Cc: [hidden email]<mailto:[hidden email]>
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" <[hidden email]<mailto:[hidden email]>> 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:[hidden email]<http://bx.psu.edu>]
Sent: Friday, February 28, 2014 4:59 PM
To: Briand, Sheldon
Cc: [hidden email]<mailto:[hidden email]>
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" <[hidden email]<mailto:[hidden email]>> 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:[hidden email]]
Sent: Friday, February 28, 2014 11:04 AM
To: Briand, Sheldon
Cc: [hidden email]<mailto:[hidden email]>
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" <[hidden email]<mailto:[hidden email]>> 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: [hidden email]<mailto:[hidden email]> [mailto:[hidden email]<mailto:[hidden email]>] On Behalf Of Briand, Sheldon
Sent: Thursday, February 27, 2014 8:18 PM
To: [hidden email]<mailto:[hidden email]>
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
[hidden email]<mailto:[hidden email]>

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: tool trouble

Briand, Sheldon
Hi,

I've finally figured out what is happening with galaxy on my end regarding tools not showing up in the menu.  I moved my install to a new larger file system and started from scratch wiping out the database to rule out my having messed up the galaxy instance.

The first tool I tried was one I had "successfully" installed on my previous setup.  I tried to install package_cufflinks_2_1_1.  One thing I noticed during the initial install setup screens is that it didn't ask me where I wanted to put the cufflinks tool in my menu.  After the package had successfully installed the tool does not show up in the Analyze data tool list.

I then tried to install the cufflinks tool which has the repository dependency of package_cufflinks_2_1_1.  During the initial install screens I'm given the option of putting the tool in one of my existing tool panel sections or adding a new one.  I installed and the tool shows up in the Analyze Data tool list where it's expected.

I'm just wondering if this is expected behavior or it's something I've configured wrong.  In cases such as bowtie 1 (I could use bowtie 0_12_7 and use the bowtie wrapper), I only have the package option and so I can't get the tool to appear in my menu.

Thanks!
-Sheldon

-----Original Message-----
From: Briand, Sheldon
Sent: Monday, March 03, 2014 2:16 PM
To: 'Greg Von Kuster'
Subject: RE: [galaxy-dev] tool trouble

Hi,

Not sure if you were still scratching your head about this one.  I am going to be moving my galaxy install to a new larger file system and put it in production so I thought I would do a new install as my current one was just testing.  If you were still going to be looking at it don't bother.  Thanks for all you had done on it up to now.

Cheers!
-Sheldon

-----Original Message-----
From: Briand, Sheldon
Sent: Friday, February 28, 2014 6:38 PM
To: 'Greg Von Kuster'
Cc: [hidden email]
Subject: RE: [galaxy-dev] tool trouble

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: [hidden email] [[hidden email]] On Behalf Of Briand, Sheldon [[hidden email]]
Sent: Friday, February 28, 2014 6:02 PM
To: 'Greg Von Kuster'
Cc: [hidden email]
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:[hidden email]]
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" <[hidden email]<mailto:[hidden email]>> 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:[hidden email]<http://bx.psu.edu>]
Sent: Friday, February 28, 2014 5:19 PM
To: Briand, Sheldon
Cc: [hidden email]<mailto:[hidden email]>
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" <[hidden email]<mailto:[hidden email]>> 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:[hidden email]<http://bx.psu.edu>]
Sent: Friday, February 28, 2014 4:59 PM
To: Briand, Sheldon
Cc: [hidden email]<mailto:[hidden email]>
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" <[hidden email]<mailto:[hidden email]>> 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:[hidden email]]
Sent: Friday, February 28, 2014 11:04 AM
To: Briand, Sheldon
Cc: [hidden email]<mailto:[hidden email]>
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" <[hidden email]<mailto:[hidden email]>> 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: [hidden email]<mailto:[hidden email]> [mailto:[hidden email]<mailto:[hidden email]>] On Behalf Of Briand, Sheldon
Sent: Thursday, February 27, 2014 8:18 PM
To: [hidden email]<mailto:[hidden email]>
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
[hidden email]<mailto:[hidden email]>

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: tool trouble

Greg Von Kuster
Hello Sheldon,


On Mar 7, 2014, at 2:14 PM, "Briand, Sheldon" <[hidden email]> wrote:

> Hi,
>
> I've finally figured out what is happening with galaxy on my end regarding tools not showing up in the menu.  I moved my install to a new larger file system and started from scratch wiping out the database to rule out my having messed up the galaxy instance.
>
> The first tool I tried was one I had "successfully" installed on my previous setup.  I tried to install package_cufflinks_2_1_1.  One thing I noticed during the initial install setup screens is that it didn't ask me where I wanted to put the cufflinks tool in my menu.  After the package had successfully installed the tool does not show up in the Analyze data tool list.

The above repository contains only a recipe for installing a tool dependency, specifically version 2.1.1 of the cufflinks package.  This installed package can be used by Galaxy tools that are containe din other repositories you may install.  The reason you were not asked which tool sections to use is because the repository does not contain any tools.


>
> I then tried to install the cufflinks tool which has the repository dependency of package_cufflinks_2_1_1.  During the initial install screens I'm given the option of putting the tool in one of my existing tool panel sections or adding a new one.  I installed and the tool shows up in the Analyze Data tool list where it's expected.

Again, the above behavior is due to the fact that you installed a repository that contained a tool, not just a tool dependency.


>
> I'm just wondering if this is expected behavior or it's something I've configured wrong.  

It is expected behavior.  Usually you would have just elected to install the repository that contains the cufflinks tool itself and checked the checkbox to install all of its repository and tool dependencies rather than doing this in separate steps.


> In cases such as bowtie 1 (I could use bowtie 0_12_7 and use the bowtie wrapper), I only have the package option and so I can't get the tool to appear in my menu.

Again, you'll see the page asking you what tool panel section you want tools contained in the repository to show up in only if the repository contains tools for display in the tool panel.  I think you may be confusing Galaxy tools with tool dependencies.


>
> Thanks!
> -Sheldon
>
> -----Original Message-----
> From: Briand, Sheldon
> Sent: Monday, March 03, 2014 2:16 PM
> To: 'Greg Von Kuster'
> Subject: RE: [galaxy-dev] tool trouble
>
> Hi,
>
> Not sure if you were still scratching your head about this one.  I am going to be moving my galaxy install to a new larger file system and put it in production so I thought I would do a new install as my current one was just testing.  If you were still going to be looking at it don't bother.  Thanks for all you had done on it up to now.
>
> Cheers!
> -Sheldon
>
> -----Original Message-----
> From: Briand, Sheldon
> Sent: Friday, February 28, 2014 6:38 PM
> To: 'Greg Von Kuster'
> Cc: [hidden email]
> Subject: RE: [galaxy-dev] tool trouble
>
> 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: [hidden email] [[hidden email]] On Behalf Of Briand, Sheldon [[hidden email]]
> Sent: Friday, February 28, 2014 6:02 PM
> To: 'Greg Von Kuster'
> Cc: [hidden email]
> 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:[hidden email]]
> 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" <[hidden email]<mailto:[hidden email]>> 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:[hidden email]<http://bx.psu.edu>]
> Sent: Friday, February 28, 2014 5:19 PM
> To: Briand, Sheldon
> Cc: [hidden email]<mailto:[hidden email]>
> 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" <[hidden email]<mailto:[hidden email]>> 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:[hidden email]<http://bx.psu.edu>]
> Sent: Friday, February 28, 2014 4:59 PM
> To: Briand, Sheldon
> Cc: [hidden email]<mailto:[hidden email]>
> 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" <[hidden email]<mailto:[hidden email]>> 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:[hidden email]]
> Sent: Friday, February 28, 2014 11:04 AM
> To: Briand, Sheldon
> Cc: [hidden email]<mailto:[hidden email]>
> 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" <[hidden email]<mailto:[hidden email]>> 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: [hidden email]<mailto:[hidden email]> [mailto:[hidden email]<mailto:[hidden email]>] On Behalf Of Briand, Sheldon
> Sent: Thursday, February 27, 2014 8:18 PM
> To: [hidden email]<mailto:[hidden email]>
> 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
> [hidden email]<mailto:[hidden email]>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this and other Galaxy lists, please use the interface at:
> http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/