Re: [galaxy-dev] Error resolving Emboss tool dependencies
We ran into similar issue again with the Bowtie. Unfortunately, with Bowtie the
re-install didn't fix the problem as it's skipping tool-sependency
re-installation.
I suspect this happened after it's tool-wrapper update. Both Emboss and Bowtie
were moved to tool-shed using tool-shed migration scripts. Has anyone else seen
similar problem before?
--
Thanks,
Shantanu
On Aug 19, 2013, at 2:26 PM, Shantanu Pavgi (Campus) wrote:
Thanks for the reply Dave.The reinstallation process worked fine, but it gave
couple of errors.
Initially it failed with a JavaScript alert like 'Initializing repository
installation failed', but resulted in following database changes.
{{{
galaxydev= select id,name,includes_datatypes,
changeset_revision,installed_changeset_revision, update_available, deleted,
uninstalled, dist_to_shed, ctx_rev, status, error_message from
tool_shed_repository where name='emboss_5' order by id;
id | name | includes_datatypes | changeset_revision |
installed_changeset_revision | update_available | deleted | uninstalled |
dist_to_shed | ctx_rev | status | error_message
+--+++--+--+-+-+--+-++---
3 | emboss_5 | f | 7334f6d0ac17 | 7334f6d0ac17
| f| f | f | t| 4
| New|
28 | emboss_5 | f | c159a6ded912 | c159a6ded912
| f| f | f | f| 4
| New|
(2 rows)
}}}
It changed old tool's (id # 3) installed changeset revision and created an
additional tool entry (id # 28). Both tools showed up in 'Manage installed
tool-shed repositories' search with Active status (Installation status: New).
Then I selected latest emboss_5 tool entry for installation which resulted in
'Initializing repository installation failed' alert once again, but the
installation was working fine under the hood. The EMBOSS tool installation
completed without any errors, however, tools didn't get placed under any
EMBOSS section (directly available - tool name/id appears as section). I will
try reinstalling it again and see if it resolves the problem.
Also, can I keep old emboss_5 as it is?
--
Shantanu
On Aug 16, 2013, at 3:43 PM, Dave Bouvier wrote:
Shantanu,
My recommendation at this point would be to reinstall the emboss_5
repository using the following procedure:
- Select deactivate or uninstall from the dropdown menu.
- Check the box to uninstall.
- When this completes, use the advanced search from the manage installed
repositories page to find the uninstalled repository.
- Select activate or reinstall from the dropdown.
- Proceed with the installation process.
--Dave B.
On 8/16/13 15:45:11.000, Shantanu Pavgi (Campus) wrote:
The installed dependencies is failing as following query in
'./lib/galaxy/tools/__init__.py' isn't returning any results.
{{{
@property
def tool_shed_repository( self ):
# If this tool is included in an installed tool shed repository,
return it.
if self.tool_shed:
return
shed_util_common.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision(
self.app,
self.tool_shed,
self.repository_name,
self.repository_owner,
self.installed_changeset_revision )
return None
}}}
The installed changeset revision used in this query is c159a6ded912.
The emboss installation on file-system has following path
'shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/7334f6d0ac17/emboss_5'.
It's current Hg revision is c159a6ded912:
{{{
$ hg id
c159a6ded912 tip
}}}
The database has following entry for emboss:
{{{
galaxy= select id, tool_shed, name, owner, dist_to_shed,
changeset_revision, installed_changeset_revision, ctx_rev from
tool_shed_repository where id=3;
id | tool_shed| name | owner | dist_to_shed |
changeset_revision | installed_changeset_revision | ctx_rev
++--+-+--++--+-
3 | toolshed.g2.bx.psu.edu | emboss_5 | devteam | t|
c159a6ded912 | 7334f6d0ac17 | 4
(1 row)
}}}
So there is a mismatch between
Re: [galaxy-dev] Error resolving Emboss tool dependencies
Thanks for the reply Dave.The reinstallation process worked fine, but it gave
couple of errors.
Initially it failed with a JavaScript alert like 'Initializing repository
installation failed', but resulted in following database changes.
{{{
galaxydev= select id,name,includes_datatypes,
changeset_revision,installed_changeset_revision, update_available, deleted,
uninstalled, dist_to_shed, ctx_rev, status, error_message from
tool_shed_repository where name='emboss_5' order by id;
id | name | includes_datatypes | changeset_revision |
installed_changeset_revision | update_available | deleted | uninstalled |
dist_to_shed | ctx_rev | status | error_message
+--+++--+--+-+-+--+-++---
3 | emboss_5 | f | 7334f6d0ac17 | 7334f6d0ac17
| f| f | f | t| 4 |
New|
28 | emboss_5 | f | c159a6ded912 | c159a6ded912
| f| f | f | f| 4 |
New|
(2 rows)
}}}
It changed old tool's (id # 3) installed changeset revision and created an
additional tool entry (id # 28). Both tools showed up in 'Manage installed
tool-shed repositories' search with Active status (Installation status: New).
Then I selected latest emboss_5 tool entry for installation which resulted in
'Initializing repository installation failed' alert once again, but the
installation was working fine under the hood. The EMBOSS tool installation
completed without any errors, however, tools didn't get placed under any EMBOSS
section (directly available - tool name/id appears as section). I will try
reinstalling it again and see if it resolves the problem.
Also, can I keep old emboss_5 as it is?
--
Shantanu
On Aug 16, 2013, at 3:43 PM, Dave Bouvier wrote:
Shantanu,
My recommendation at this point would be to reinstall the emboss_5 repository
using the following procedure:
- Select deactivate or uninstall from the dropdown menu.
- Check the box to uninstall.
- When this completes, use the advanced search from the manage installed
repositories page to find the uninstalled repository.
- Select activate or reinstall from the dropdown.
- Proceed with the installation process.
--Dave B.
On 8/16/13 15:45:11.000, Shantanu Pavgi (Campus) wrote:
The installed dependencies is failing as following query in
'./lib/galaxy/tools/__init__.py' isn't returning any results.
{{{
@property
def tool_shed_repository( self ):
# If this tool is included in an installed tool shed repository,
return it.
if self.tool_shed:
return
shed_util_common.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision(
self.app,
self.tool_shed,
self.repository_name,
self.repository_owner,
self.installed_changeset_revision )
return None
}}}
The installed changeset revision used in this query is c159a6ded912.
The emboss installation on file-system has following path
'shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/7334f6d0ac17/emboss_5'.
It's current Hg revision is c159a6ded912:
{{{
$ hg id
c159a6ded912 tip
}}}
The database has following entry for emboss:
{{{
galaxy= select id, tool_shed, name, owner, dist_to_shed,
changeset_revision, installed_changeset_revision, ctx_rev from
tool_shed_repository where id=3;
id | tool_shed| name | owner | dist_to_shed |
changeset_revision | installed_changeset_revision | ctx_rev
++--+-+--++--+-
3 | toolshed.g2.bx.psu.edu | emboss_5 | devteam | t|
c159a6ded912 | 7334f6d0ac17 | 4
(1 row)
}}}
So there is a mismatch between installed_changeset_revision in the database
and the one being queried. I think the one used in the query is obtained
from migrated_tools_conf.xml file.
{{{
tool_shedtoolshed.g2.bx.psu.edu/tool_shed
repository_nameemboss_5/repository_name
repository_ownerdevteam/repository_owner
installed_changeset_revisionc159a6ded912/installed_changeset_revision
Re: [galaxy-dev] Error resolving Emboss tool dependencies
Hi Shantanu, can you have a look in the Admin menu if EMBOSS is installed correctly (green) or if it failed (red)? Thanks, Bjoern I have migrated Emboss tool from dist to tool-shed using the migration script and later updated it's revision. The tool was installed along with it's dependencies, but it's failing to find them during job run. It's logging following 'Failed to resolve dependency on 'emboss', ignoring' warning message in the log file. It seems like build_dependency_shell_commands method in '/lib/galaxy/tools/__init__.py' is unable to get installed_tool_dependencies. I am not sure why this would fail and how to resolve it. I have tried resetting tool metadata several times, but that didn't help. Appreciate any help on resolving this error. I am using Galaxy release_2013.06.03 revision. Thanks, Shantanu ___ 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/
Re: [galaxy-dev] Error resolving Emboss tool dependencies
Thanks for the reply Bjoern. It's installed correctly - green box. The emboss entries in tool_dependency and tool_shed_repository look fine as well. If I directly run an emboss command (e.g. antigenic) from CLI then it seems to be working. -- Shantanu On Aug 15, 2013, at 2:53 PM, Björn Grüning wrote: Hi Shantanu, can you have a look in the Admin menu if EMBOSS is installed correctly (green) or if it failed (red)? Thanks, Bjoern I have migrated Emboss tool from dist to tool-shed using the migration script and later updated it's revision. The tool was installed along with it's dependencies, but it's failing to find them during job run. It's logging following 'Failed to resolve dependency on 'emboss', ignoring' warning message in the log file. It seems like build_dependency_shell_commands method in '/lib/galaxy/tools/__init__.py' is unable to get installed_tool_dependencies. I am not sure why this would fail and how to resolve it. I have tried resetting tool metadata several times, but that didn't help. Appreciate any help on resolving this error. I am using Galaxy release_2013.06.03 revision. Thanks, Shantanu ___ 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/
Re: [galaxy-dev] Error resolving Emboss tool dependencies
Hi, Thanks for the reply Bjoern. It's installed correctly - green box. The emboss entries in tool_dependency and tool_shed_repository look fine as well. If I directly run an emboss command (e.g. antigenic) from CLI then it seems to be working. can you check a few things or paste the complete warning message from Failed to resolve dependency on 'emboss'? - Do you have more than one EMBOSS suite installed or showing up in your Tool Panel? - Which version is shown if you run some EMBOSS tools? - I assume tool shed, or test tool shed? - can you give us the revision number of EMBOSS that is installed? Thanks, Bjoern -- Shantanu On Aug 15, 2013, at 2:53 PM, Björn Grüning wrote: Hi Shantanu, can you have a look in the Admin menu if EMBOSS is installed correctly (green) or if it failed (red)? Thanks, Bjoern I have migrated Emboss tool from dist to tool-shed using the migration script and later updated it's revision. The tool was installed along with it's dependencies, but it's failing to find them during job run. It's logging following 'Failed to resolve dependency on 'emboss', ignoring' warning message in the log file. It seems like build_dependency_shell_commands method in '/lib/galaxy/tools/__init__.py' is unable to get installed_tool_dependencies. I am not sure why this would fail and how to resolve it. I have tried resetting tool metadata several times, but that didn't help. Appreciate any help on resolving this error. I am using Galaxy release_2013.06.03 revision. Thanks, Shantanu ___ 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/
