Re: [galaxy-dev] Improved Workflows through Multiple File Datasets

[Jorrit Boekel]

If one could upvote pull request, I'd be doing that now!

thanks loads John,
jorrit

On 12/05/2012 07:14 PM, John Chilton wrote:

Here is my video-based sales pitch for multiple file datasets
(specifically pull request 86 and 87 and subsequent future pull
requests).

http://www.youtube.com/watch?v=DxJzEkOasu4

I am still committed to helping develop a comprehensive tag-based
approach to enhanced workflows with normal datasets, but that seems
months off at best and this current approach has the great feature of
tracking "sample" names throughout complex workflows.

Thanks for your time,
-John


John Chilton
Senior Software Developer
University of Minnesota Supercomputing Institute
Office: 612-625-0917
Cell: 612-226-9223
Bitbucket: https://bitbucket.org/jmchilton
Github: https://github.com/jmchilton
Web: http://jmchilton.net
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--
Scientific programmer
Mass spec analysis support @ BILS
Janne Lehtiö / Lukas Käll labs
SciLifeLab Stockholm

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Re: [galaxy-dev] Permission denied error for velveth

[Andreas Kuntzagk]

Sorry, I think I had not really restarted galaxy after making the change.
After I changed some logging options in universe_wsgi.ini and restarted it's 
suddenly working.
So I can confirm your fix works.

Thank you for your help.

Andreas

On 05.12.2012 13:40, Andreas Kuntzagk wrote:

Hi,

Does not work for me. I still get the same error.
If you need me to run more test, just email me.

regards, Andreas

On 04.12.2012 18:27, John Chilton wrote:

I don't have a velvet or a submit-jobs-as-user environment setup so I
cannot test this, but it seems like this should have a an easy fix.
Can someone who is experiencing the problem try the attached patch or
has something like this been tried and there is some other problem?

-John

(09:43:01 AM) jmchilton: Is the velvet problem related to something
specific about how velvet runs or do no tools that depend on
extra_files_path work with as-user jobs?
(10:10:31 AM) natefoo: they have to either write to files_path or
extra_files_path, let me find the email...
(10:12:24 AM) natefoo:
http://dev.list.galaxyproject.org/Folder-permissions-after-cluster-run-td4657156.html#a4657219
(10:12:26 AM) mrscribe: Title: Galaxy Development List Archive -
Folder permissions after cluster run (at dev.list.galaxyproject.org)
(11:07:31 AM) jmchilton: Is fixing the velvet problem as simple as
changing extra_files_path to files_path in the wrappers then?

On Tue, Dec 4, 2012 at 9:38 AM, Oleksandr Moskalenko  wrote:


On Dec 4, 2012, at 9:30 AM, Andreas Kuntzagk  
wrote:


I see that this issue came up before by Oleksandr Moskalenko in October but was 
unresolved then.
Is there a workaround now?

regards, Andreas


The velvet wrapper is not going to be usable for real user jobs until someone 
rewrites it to work
without direct manipulation of files in the database/ tree. No work has been 
done on this nor any
is planned as far as I know.

Regards,

Alex
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--
Andreas Kuntzagk

SystemAdministrator

Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str. 10, 13125 Berlin, Germany

http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich
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[galaxy-dev] rgFastQC.py error

[dengyongyilong]

Hi all,
  when I use the tool "FastQC:Read QC" I got the next index:
 "An error occurred running this job: Traceback (most recent call last): File 
"/home/galaxy/galaxy-dist/tools/rgenetics/rgFastQC.py", line 158, in assert   
os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable 
%s' % opts.executable AssertionError: ##rgFast".
 
Could you help me to solve this?

look forward to your reply!

best regards!

发件人： dengyongyilong
发送时间： 2012-12-06 09:20
收件人： James Taylor; Guest, Simon
抄送： galaxy-dev@lists.bx.psu.edu
主题： Re: Re: [galaxy-dev] RPy testsuite some tests passing - enough for Galaxy?
Hi,I want learn how to use the tool "BOWtie 2",Could you tell me where can I 
find the tutorial?
Thanks!

best regards to you!



dengyongyilong

From: James Taylor
Date: 2012-12-06 00:02
To: Guest, Simon
CC: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] RPy testsuite some tests passing - enough for Galaxy?
Rpy is only used by a handful of tools (should be listed on the tool
dependencies page). Everything else in Galaxy should work fine without
it.
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Re: [galaxy-dev] Permission denied error for velveth

[Andreas Kuntzagk]

Ok,

while velveth seems to work now, if I put the result into velvetg I get another 
error:

Traceback (most recent call last):
  File "/data/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 175, 
in queue_job
job_wrapper.prepare()
  File "/data/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 184, in 
prepare
self.command_line = self.tool.build_command_line( param_dict )
  File "/data/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 2424, in 
build_command_line
command_line = fill_template( self.command, context=param_dict )
  File "/data/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in 
fill_template
return str( Template( source=template_text, searchList=[context] ) )
  File 
"/data/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 
1004, in __str__

return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1354790596_63_67504.py", 
line 84, in respond
NotFound: cannot find 'files_path' while searching for 'input.files_path'

Andreas

On 06.12.2012 10:52, Andreas Kuntzagk wrote:

Sorry, I think I had not really restarted galaxy after making the change.
After I changed some logging options in universe_wsgi.ini and restarted it's 
suddenly working.
So I can confirm your fix works.

Thank you for your help.

Andreas

On 05.12.2012 13:40, Andreas Kuntzagk wrote:

Hi,

Does not work for me. I still get the same error.
If you need me to run more test, just email me.

regards, Andreas

On 04.12.2012 18:27, John Chilton wrote:

I don't have a velvet or a submit-jobs-as-user environment setup so I
cannot test this, but it seems like this should have a an easy fix.
Can someone who is experiencing the problem try the attached patch or
has something like this been tried and there is some other problem?

-John

(09:43:01 AM) jmchilton: Is the velvet problem related to something
specific about how velvet runs or do no tools that depend on
extra_files_path work with as-user jobs?
(10:10:31 AM) natefoo: they have to either write to files_path or
extra_files_path, let me find the email...
(10:12:24 AM) natefoo:
http://dev.list.galaxyproject.org/Folder-permissions-after-cluster-run-td4657156.html#a4657219
(10:12:26 AM) mrscribe: Title: Galaxy Development List Archive -
Folder permissions after cluster run (at dev.list.galaxyproject.org)
(11:07:31 AM) jmchilton: Is fixing the velvet problem as simple as
changing extra_files_path to files_path in the wrappers then?

On Tue, Dec 4, 2012 at 9:38 AM, Oleksandr Moskalenko  wrote:


On Dec 4, 2012, at 9:30 AM, Andreas Kuntzagk  
wrote:


I see that this issue came up before by Oleksandr Moskalenko in October but was 
unresolved then.
Is there a workaround now?

regards, Andreas


The velvet wrapper is not going to be usable for real user jobs until someone 
rewrites it to work
without direct manipulation of files in the database/ tree. No work has been 
done on this nor any
is planned as far as I know.

Regards,

Alex
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--
Andreas Kuntzagk

SystemAdministrator

Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str. 10, 13125 Berlin, Germany

http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich
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Re: [galaxy-dev] Permission denied error for velveth

[John Chilton]

Was velveth working prior to the patch (i.e. is it okay to use
extra_files_path on outputs?) or does some more work need to be done
at the infrastructure level to copy output extra files over in
run-as-user mode?

-John

On Thu, Dec 6, 2012 at 4:52 AM, Andreas Kuntzagk
 wrote:
> Ok,
>
> while velveth seems to work now, if I put the result into velvetg I get
> another error:
>
> Traceback (most recent call last):
>   File "/data/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line
> 175, in queue_job
> job_wrapper.prepare()
>   File "/data/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 184, in
> prepare
> self.command_line = self.tool.build_command_line( param_dict )
>   File "/data/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 2424,
> in build_command_line
> command_line = fill_template( self.command, context=param_dict )
>   File "/data/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in
> fill_template
> return str( Template( source=template_text, searchList=[context] ) )
>   File
> "/data/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py",
> line 1004, in __str__
> return getattr(self, mainMethName)()
>   File "cheetah_DynamicallyCompiledCheetahTemplate_1354790596_63_67504.py",
> line 84, in respond
> NotFound: cannot find 'files_path' while searching for 'input.files_path'
>
> Andreas
>
>
> On 06.12.2012 10:52, Andreas Kuntzagk wrote:
>>
>> Sorry, I think I had not really restarted galaxy after making the change.
>> After I changed some logging options in universe_wsgi.ini and restarted
>> it's suddenly working.
>> So I can confirm your fix works.
>>
>> Thank you for your help.
>>
>> Andreas
>>
>> On 05.12.2012 13:40, Andreas Kuntzagk wrote:
>>>
>>> Hi,
>>>
>>> Does not work for me. I still get the same error.
>>> If you need me to run more test, just email me.
>>>
>>> regards, Andreas
>>>
>>> On 04.12.2012 18:27, John Chilton wrote:

 I don't have a velvet or a submit-jobs-as-user environment setup so I
 cannot test this, but it seems like this should have a an easy fix.
 Can someone who is experiencing the problem try the attached patch or
 has something like this been tried and there is some other problem?

 -John

 (09:43:01 AM) jmchilton: Is the velvet problem related to something
 specific about how velvet runs or do no tools that depend on
 extra_files_path work with as-user jobs?
 (10:10:31 AM) natefoo: they have to either write to files_path or
 extra_files_path, let me find the email...
 (10:12:24 AM) natefoo:

 http://dev.list.galaxyproject.org/Folder-permissions-after-cluster-run-td4657156.html#a4657219
 (10:12:26 AM) mrscribe: Title: Galaxy Development List Archive -
 Folder permissions after cluster run (at dev.list.galaxyproject.org)
 (11:07:31 AM) jmchilton: Is fixing the velvet problem as simple as
 changing extra_files_path to files_path in the wrappers then?

 On Tue, Dec 4, 2012 at 9:38 AM, Oleksandr Moskalenko 
 wrote:
>
>
> On Dec 4, 2012, at 9:30 AM, Andreas Kuntzagk
>  wrote:
>
>> I see that this issue came up before by Oleksandr Moskalenko in
>> October but was unresolved then.
>> Is there a workaround now?
>>
>> regards, Andreas
>
>
> The velvet wrapper is not going to be usable for real user jobs until
> someone rewrites it to work
> without direct manipulation of files in the database/ tree. No work has
> been done on this nor any
> is planned as far as I know.
>
> Regards,
>
> Alex
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>http://lists.bx.psu.edu/
>>>
>>>
>>
>
> --
> Andreas Kuntzagk
>
> SystemAdministrator
>
> Berlin Institute for Medical Systems Biology at the
> Max-Delbrueck-Center for Molecular Medicine
> Robert-Roessle-Str. 10, 13125 Berlin, Germany
>
> http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich
> ___
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> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
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Re: [galaxy-dev] Re-installing error persists

[Greg Von Kuster]

Hi Franco,

Sorry you're still seeing this issue.  I assume you updated your Galaxy to the 
dist release, so not sure how you have rev 8359 - we haven't even reached that 
rev in development yet.  However, since you've updated, the cause of the 
problem is narrowed down to likely being one of the weaknesses of the mysql 
database (this is why I always recommend using postgres over mysql).

We don't have a script to execute sql statements to correct problems like this 
because they do not occur very frequently and they usually turn out to be 
something very specific to the local environment,  However, looking at your 
contra repository, it looks like it attempts to install only 1 tool dependency 
(bedtools), so it should be fairly easy to fix manually.

Step 1:
You need to get the record of the installed tool shed repository named contra 
from your Galaxy database (you'll need the value for Step 3).  This should do 
it for you.

select * from tool_shed_repository where name = 'contra';  (Keep track of the 
id column value for Step 3 below)

Step 2:
Now update the row using the following sql statement:

update tool_shed_repository set deleted = True, uninstalled = True where name = 
'contra';

Step 3:
Using the value in the id column from Step 1, execute the following sql, 
substituting that value - capitalization in the status value is required, so 
use the exact value.

update tool_dependency set status = 'Uninstalled' where tool_shed_repository_id 
= ;

Step 4:
Manually edit the shed_tool_conf.xml file to remove the entry for the contra 
repository

This should be all you need to do.  Let me know if you bump into additional 
issues.

Greg Von Kuster


On Dec 6, 2012, at 2:08 AM, Franco Caramia wrote:

> Hi Greg,
> 
> We have now pulled the lastest revision 8359:c08a5d0d2a4f but the problem 
> persists. The stack trace remains the same... 
> Any ideas on what could be happening?
> Ideally we would like to be able to fix the problem through the galaxy 
> interface, but in case we find no solution, do galaxy devs have some repo for 
> MySQL scripts to “clean” the DB?? (ex. Complete delete of a toolshed tool)..
> 
> 
> Thanks,  
> 
> 
> On 5/12/12 9:10 PM, "Greg Von Kuster"  wrote:
> 
>> If you have not yet updated your Galaxy instance to the revision from the 
>> galaxy-dist repository in bitbucket, then that is most likely the cause of 
>> the behavior you are seeing.
>> 
>> Greg Von Kuster
>> 
>> On Dec 5, 2012, at 12:52 AM, Franco Caramia wrote:
>> 
>>> Re-installing error persists 
>>> 
>>> 
>>> Hi Greg,
>>> 
>>> I have now modified the tool_dependencies.xml thank you for that..
>>> 
>>> I still have problems re-installing the tool... (need to reinstall to 
>>> update the tool dependency and test it correctly)
>>> 
>>> Is the reinstalling failure related to my galaxy version?? 
>>> 
>>> Here is the error:
>>> Server Error
>>>  URL: 
>>> http://bioinf-galaxy/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a
>>> Module paste.exceptions.errormiddleware:143 in __call__
>>> >>   
>>> >> 
>>> >>  app_iter = self.application(environ, start_response)
>>> Module paste.debug.prints:98 in __call__
>>> >>   
>>> >> 
>>> >>  environ, self.app)
>>> Module paste.wsgilib:539 in intercept_output
>>> >>   
>>> >> 
>>> >>  app_iter = application(environ, replacement_start_response)
>>> Module paste.recursive:80 in __call__
>>> >>   
>>> >> 
>>> >>  return self.application(environ, start_response)
>>> Module paste.httpexceptions:632 in __call__
>>> >>   
>>> >> 
>>> >>  return self.application(environ, start_response)
>>> Module galaxy.web.framework.base:160 in __call__
>>> >>   
>>> >> 
>>> >>  body = method( trans, **kwargs )
>>> Module galaxy.web.framework:184 in decorator
>>> >>   
>>> >> 
>>> >>  return func( self, trans, *args, **kwargs )
>>> Module galaxy.web.controllers.admin_toolshed:350 in browse_repositories
>>> >>   
>>> >> 
>>> >>  return self.reselect_tool_panel_section( trans, **kwd )
>>> Module galaxy.web.framework:184 in decorator
>>> >>   
>>> >> 

[galaxy-dev] Problem in Manage data Library

[Sachit Adhikari]

We have found that, in Galaxy, when we add dataset to a library under
Manage data libraries, Galaxy sometimes detects the type of the file and
sometimes does not. What I have noticed is that it detects the type of the
file when we select "Copy file into Galaxy" under "Copy data into Galaxy?"
option and does not detect it when we select "Link to files ..." Is this a
known issue?

Regards,
Sachit
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[galaxy-dev] local instance upload data failed

[刘阳]

I just installed postgres, and modified the database_connection option
in universe_wsgi.ini
 to database_connection = postgres://postgres:postgres@localhost:5432/galaxy

Then I tried to upload a fasta format file (about 4KB), what confused me is
that it is uploading on and on. I think the uploading process is pending.
The console gave a lot of message like this:

127.0.0.1 - - [06/Dec/2012:12:10:01 +0800] "GET
/api/histories/f2db41e1fa331b3e HTTP/1.1" 200 - "
http://127.0.0.1:8080/history"; "Mozilla/5.0 (X11; Linux i686)
AppleWebKit/536.11 (KHTML, like Gecko) Ubuntu/12.04 Chromium/20.0.1132.47
Chrome/20.0.1132.47 Safari/536.11"

Is it caused by the wrong configuration of postgres? I can't figure it out.
Does anyone encountered similar problem?

Jacky Lau
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Re: [galaxy-dev] Problem in Manage data Library

[Anthonius deBoer]

I have a similar problem in the latest galaxy-dist version from Dec 3rd.When I run BWA or BOWTIE2 (but it probably is not limited to those) the resulting SAM/BAM file is shown to be empty and none of the metadata has been updated.When I do a manual "Auto-detect" in the "Edit Attributes" section of the dataset, it correctly detects the size and other metadata of the  dataset...It seems to me that the set metadata is not running after a dataset is produced.I tried both set_metadata_externally = True and set_metadata_externally = False but this did not make a difference...Any ideas?Thanks,ThonOn Dec 06, 2012, at 04:03 AM, Sachit Adhikari  wrote:We have found that, in Galaxy, when we add dataset to a library under Manage data libraries, Galaxy sometimes detects the type of the file and sometimes does not. What I have noticed is that it detects the type of the file when we select "Copy file into Galaxy" under "Copy data into Galaxy?" option and does not detect it when we select "Link to files ..." Is this a known issue?Regards,Sachit___ 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/___
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[galaxy-dev] Which tools do I need to install?

[greg]

Hi guys,

I've finished a local galaxy install on our cluster but I'm confused
as to which tools are not included and how I need to install them.

I saw this page:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

But how do I tell what is not installed yet?

And where do I install everything I'll need?  In galaxy-dist
somewhere?  Or will that interfere with code updates?

Thanks,

Greg
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[galaxy-dev] How to Install FastQC?

[greg]

I'm guessing FastQC isn't installed by default?

This page give these instructions:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

FastQC (0.10.0)NGS: QC and manipulationFastQC from Babraham. The main
fastqc perl script must be executable from
tool-data/shared/jars/FastQC/fastqc

But I don't understand what it means. Do I need to download something,
change permissions?  I don't have anything inside the jars folder.

Thanks,

Greg
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[galaxy-dev] Defunct munge processes using Torque PBS

[Matthew Shirley]

I am fairly new to PBS management, so I can't rule out some misconfiguration, 
but I have a strange issue when running Galaxy with the PBS job runner. It 
seems that munge spawns a bunch of defunct processes after running Galaxy on my 
cluster:

`ps axjf`:

1 25992 25991 25991 ?   -1 Sl   7   8:48 python 
./scripts/paster.py serve universe_wsgi.ini --daemon
25992 26032 25991 25991 ?   -1 Z7   0:00  \_ [munge] 
25992 26034 25991 25991 ?   -1 Z7   0:00  \_ [munge] 
25992 26036 25991 25991 ?   -1 Z7   0:00  \_ [munge] 

Now, these processes are being spawned by Galaxy, and I can't figure out why. 
Can anyone provide some insight or clues about where to start debugging this? 
Thanks,

Matt

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Re: [galaxy-dev] How to Install FastQC?

[Anthonius deBoer]

Hi Greg,Indeed you need to install many many tools to make galaxy run.You may be better off getting the cloud version, which has many tools already installed.Getting GALAXY to run with all the tools that are provided is not a trivial task...It gets MUCH better with the TOOLSHED option, since this can install many of the tools you may need...the "old" way of galaxy was to rely on many of the tools to be available on the path so they magically run, but things like GATK and FASTQC etc. that are run from JAVA jars, need to be installed manually into that directory tool-data/shared/jarsThonOn Dec 06, 2012, at 11:36 AM, greg  wrote:I'm guessing FastQC isn't installed by default?  This page give these instructions: http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies  FastQC (0.10.0)NGS: QC and manipulationFastQC from Babraham. The main fastqc perl script must be executable from tool-data/shared/jars/FastQC/fastqc  But I don't understand what it means. Do I need to download something, change permissions? I don't have anything inside the jars folder.  Thanks,  Greg ___ 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/___
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Re: [galaxy-dev] Re-installing error persists

[Franco Caramia]

Hi Greg,

Thanks a lot for your help.

I still get the same error trying to reinstall the tool...

Here is the status of the DB:

mysql> select name,id,status,deleted,uninstalled from tool_shed_repository
where name = 'contra';
+++-+-+-+
| name   | id | status  | deleted | uninstalled |
+++-+-+-+
| contra |  9 | Uninstalled |   1 |   1 |
+++-+-+-+
1 row in set (0.00 sec)

select name,status from tool_dependency where tool_shed_repository_id = 9;
+--+-+
| name | status  |
+--+-+
| bedtools | Uninstalled |
+--+-+
1 row in set (0.00 sec)

The shed_tool_conf has no Œcontra¹ entry...

A complete remove from the DB should help to solve it, but I don¹t want to
break possible relationship tables as I¹m not familiar with the schema..

Thanks,

Franco

On 7/12/12 1:01 AM, "Greg Von Kuster"  wrote:

> Hi Franco,
> 
> Sorry you're still seeing this issue.  I assume you updated your Galaxy to the
> dist release, so not sure how you have rev 8359 - we haven't even reached that
> rev in development yet.  However, since you've updated, the cause of the
> problem is narrowed down to likely being one of the weaknesses of the mysql
> database (this is why I always recommend using postgres over mysql).
> 
> We don't have a script to execute sql statements to correct problems like this
> because they do not occur very frequently and they usually turn out to be
> something very specific to the local environment,  However, looking at your
> contra repository, it looks like it attempts to install only 1 tool dependency
> (bedtools), so it should be fairly easy to fix manually.
> 
> Step 1:
> You need to get the record of the installed tool shed repository named contra
> from your Galaxy database (you'll need the value for Step 3).  This should do
> it for you.
> 
> select * from tool_shed_repository where name = 'contra';  (Keep track of the
> id column value for Step 3 below)
> 
> Step 2:
> Now update the row using the following sql statement:
> 
> update tool_shed_repository set deleted = True, uninstalled = True where name
> = 'contra';
> 
> Step 3:
> Using the value in the id column from Step 1, execute the following sql,
> substituting that value - capitalization in the status value is required, so
> use the exact value.
> 
> update tool_dependency set status = 'Uninstalled' where
> tool_shed_repository_id = ;
> 
> Step 4:
> Manually edit the shed_tool_conf.xml file to remove the entry for the contra
> repository
> 
> This should be all you need to do.  Let me know if you bump into additional
> issues.
> 
> Greg Von Kuster
> 
> 
> On Dec 6, 2012, at 2:08 AM, Franco Caramia wrote:
> 
>> Re: Re-installing error persists
>> Hi Greg,
>> 
>> We have now pulled the lastest revision 8359:c08a5d0d2a4f but the problem
>> persists. The stack trace remains the same...
>> Any ideas on what could be happening?
>> Ideally we would like to be able to fix the problem through the galaxy
>> interface, but in case we find no solution, do galaxy devs have some repo for
>> MySQL scripts to ³clean² the DB?? (ex. Complete delete of a toolshed tool)..
>> 
>> 
>> Thanks,  
>> 
>> 
>> On 5/12/12 9:10 PM, "Greg Von Kuster" >  > wrote:
>> 
>>> If you have not yet updated your Galaxy instance to the revision from the
>>> galaxy-dist repository in bitbucket, then that is most likely the cause of
>>> the behavior you are seeing.
>>> 
>>> Greg Von Kuster
>>> 
>>> On Dec 5, 2012, at 12:52 AM, Franco Caramia wrote:
>>> 
 Re-installing error persists
 
 
 Hi Greg,
 
 I have now modified the tool_dependencies.xml thank you for that..
 
 I still have problems re-installing the tool... (need to reinstall to
 update the tool dependency and test it correctly)
 
 Is the reinstalling failure related to my galaxy version??
 
 Here is the error:
 Server Error
   URL: 
 http://bioinf-galaxy/admin_toolshed/browse_repositories?operation=activate+
 or+reinstall&id=88ee2d7021e4dc1a
 Module paste.exceptions.errormiddleware:143 in __call__
>> >>   
>> > ivate+or+reinstall&id=88ee2d7021e4dc1a#> app_iter =
>> self.application(environ, start_response)
 Module paste.debug.prints:98 in __call__
>> >>   
>> > ivate+or+reinstall&id=88ee2d7021e4dc1a#> environ, self.app)
 Module paste.wsgilib:539 in intercept_output
>> >>   
>> > ivate+or+reinstall&id=88ee2d7021e4dc1a#> app_iter = application(environ,
>> replacement_start_response)
 Module paste.recursive:80 in __call__
>> >>   
>> 

[galaxy-dev] How to refresh the tool panel in Galaxy?

[Huayan Gao]

Hi,

I am trying to add a tool into Galaxy. So far everything is ok except that
I need to restart the server to make the tool showing up in the tool panel.

So my question is that how to refresh the tool panel without restarting the
server?

After I install a tool from toolshed, I can see the tool immediately from
the tool panel. This is exactly the function I want to implement in python.
I was reading the code but too complicated. Could you point me the right
place(code)?

Thanks a lot.

Best,
Huayan
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