Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

[Carl Eberhard]

Thanks much, Carlos - I owe you a beer!


On Mon, Feb 4, 2013 at 4:01 PM, Dan Tenenbaum  wrote:

> On Mon, Feb 4, 2013 at 11:45 AM, Carlos Borroto
>  wrote:
> > On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum 
> wrote:
> >>> Re: login: I believe there's a redirect in place that moves you past
> the
> >>> older 'Return to the homepage' message automatically - I think you're
> good
> >>> there (and logged in). Are you seeing the 'Logged in as '
> in the
> >>> 'User' menu at the top?
> >>>
> >>
> >> No. I think I'm not actually being logged in.
> >> All I see under the User menu is "Login" and "Register".
> >
> > I realize this is a long thread and my recommendation might not help
> > much or was done it already. Sorry if that's the case.
> >
> > This behavior is something I have seen often with Chrome in particular
> > and 99% of the time is related to an old cookie. Specially when I'm
> > accessing a different galaxy instance from the same URL I accessed a
> > previous one, something I see Dan did at the beginning of this thread.
> > I recommend erasing any cookie related to galaxy and also trying with
> > a different browser. Firefox seems to work particularly fine.
> >
>
> Indeed, it works with Firefox. And it works with Chrome after I delete
> my cookies.
>
> Thanks very much!
> Dan
>
>
> > Hope it helps,
> > Carlos
>
___
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/

Re: [galaxy-dev] File Upload doesn't generate any activity

[Hakeem Almabrazi]

HI Nicola,

I did upgrading.  It seems that error is gone now but I got these errors.  I am 
not sure if they are critical or due to my settings.
galaxy.tools WARNING 2013-02-04 14:04:02,764 A when tag has not been defined 
for 'master_variable_type (master_variable_type_selector) --> allPairs', 
assuming empty inputs.
galaxy.tools WARNING 2013-02-04 14:04:04,391 A when tag has been defined for 
'manipulation (manipulation_selector) --> modify_each_score', but does not 
appear to be selectable.
galaxy.tools.test DEBUG 2013-02-04 14:04:05,164 Error in add_param for 
report_discordant_pairs: Unable to determine parameter type of test input 
'report_discordant_pairs'. Ensure that the parameter exists and that any 
container groups are defined first.
docutils WARNING 2013-02-04 14:04:05,198 :50: (WARNING/2) Literal block 
expected; none found.

galaxy.tools.test DEBUG 2013-02-04 14:04:05,209 Error in add_param for 
min_coverage_intron: Unable to determine parameter type of test input 
'min_coverage_intron'. Ensure that the parameter exists and that any container 
groups are defined first.
galaxy.tools.test DEBUG 2013-02-04 14:04:05,209 Error in add_param for 
max_coverage_intron: Unable to determine parameter type of test input 
'max_coverage_intron'. Ensure that the parameter exists and that any container 
groups are defined first.
galaxy.tools.test DEBUG 2013-02-04 14:04:06,487 Error in add_param for force: 
Unable to determine parameter type of test input 'force'. Ensure that the 
parameter exists and that any container groups are defined first.
galaxy.tools.test DEBUG 2013-02-04 14:04:06,773 Error in add_param for input: 
Unable to determine parameter type of test input 'input'. Ensure that the 
parameter exists and that any container groups are defined first.
galaxy.tools.test DEBUG 2013-02-04 14:04:06,773 Error in add_param for 
group1_1: Unable to determine parameter type of test input 'group1_1'. Ensure 
that the parameter exists and that any container groups are defined first.
galaxy.tools.test DEBUG 2013-02-04 14:04:06,773 Error in add_param for 
group1_2: Unable to determine parameter type of test input 'group1_2'. Ensure 
that the parameter exists and that any container groups are defined first.
galaxy.tools.test DEBUG 2013-02-04 14:04:06,773 Error in add_param for 
group1_3: Unable to determine parameter type of test input 'group1_3'. Ensure 
that the parameter exists and that any container groups are defined first.
galaxy.tools.test DEBUG 2013-02-04 14:04:06,773 Error in add_param for 
group2_1: Unable to determine parameter type of test input 'group2_1'. Ensure 
that the parameter exists and that any container groups are defined first.
galaxy.tools.test DEBUG 2013-02-04 14:04:06,773 Error in add_param for 
group2_2: Unable to determine parameter type of test input 'group2_2'. Ensure 
that the parameter exists and that any container groups are defined first.
galaxy.tools.test DEBUG 2013-02-04 14:04:06,773 Error in add_param for 
group2_3: Unable to determine parameter type of test input 'group2_3'. Ensure 
that the parameter exists and that any container groups are defined first.
galaxy.tools INFO 2013-02-04 14:04:07,068 Parsing the tool configuration 
./migrated_tools_conf.xml




-Original Message-
From: Nicola Soranzo [mailto:sora...@crs4.it] 
Sent: Monday, February 04, 2013 11:52 AM
To: Hakeem Almabrazi
Cc: Galaxy Dev
Subject: Re: [galaxy-dev] File Upload doesn't generate any activity

Il giorno lun, 04/02/2013 alle 17.41 +, Hakeem Almabrazi ha
scritto: 
> Thank you Nicola,
> 
> Should I replace my current galaxy-dist with this version or is there 
> different way to upgrade?

Take a look at this wiki page:

http://wiki.galaxyproject.org/Admin/Get%
20Galaxy#Keep_your_code_up_to_date

Nicola

> -Original Message-
> From: Nicola Soranzo [mailto:sora...@crs4.it] 
> Sent: Monday, February 04, 2013 10:50 AM
> To: Hakeem Almabrazi
> Cc: Dannon Baker; Galaxy Dev
> Subject: Re: [galaxy-dev] File Upload doesn't generate any activity
> 
> Il giorno lun, 04/02/2013 alle 16.33 +, Hakeem Almabrazi ha
> scritto: 
> > Thank you Dannon.  Hopefully things should be moving forward from now on.
> > 
> > "This issue with the LWR has been fixed in changeset 8731:3299529e0fe8 
> > which will be in the next distribution release."
> > 
> > That will be awesome.
> 
> It's already in galaxy-dist since Saturday 2013/02/02, changeset
> 8531:3299529e0fe8 .
> 
> Kind Regards,
> Nicola
> 



___
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/

Re: [galaxy-dev] File Upload doesn't generate any activity

[Stephen Groenewold]

Our upload issues seem to have been resolved. Thanks for checking.

I added the attached comment to another list-serve message - we did have the 
referenced error in our startup logs. The attached email mentions I was still 
having trouble uploading files with the Upload File tool. That is now resolved 
as well.

Steve

-Original Message-
From: Dannon Baker [mailto:dannonba...@me.com] 
Sent: Sunday, February 03, 2013 7:14 PM
To: Hakeem Almabrazi
Cc: Stephen Groenewold; Galaxy Dev; galaxy-b...@bx.psu.edu Bugs
Subject: Re: [galaxy-dev] File Upload doesn't generate any activity

I just wanted to follow up on this and make sure everything was now working as 
expected.  I've tried to reproduce the original issue and have thus far been 
unsuccessful in doing so with a fresh instance.  Is the configuration of your 
Galaxy instance special in any way?  Did you notice any logged errors (either 
in the Javascript console or in Galaxy's log)?

-Dannon


On Feb 1, 2013, at 3:37 PM, Hakeem Almabrazi  wrote:

> Stephen,,,
>  
> Here is your solution:
>  
> In the Tools panel select "Get Data", "Upload File". You can either upload a 
> file, or enter one or more URLs in the "URL/Text" box. Enter 
> "http://galaxy.psu.edu/CPMB/TAF1_ChIP.txt"; in the box and click "Execute"
>  
> I am not sure what happened there but it seems this triggered some database 
> updates that was needed. 
>  
> It worked J
>  
>  
> From: galaxy-dev-boun...@lists.bx.psu.edu 
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Stephen 
> Groenewold
> Sent: Friday, February 01, 2013 10:41 AM
> To: galaxy-dev@lists.bx.psu.edu
> Subject: [galaxy-dev] File Upload doesn't generate any activity
>  
> We've  installed a local instance of Galaxy and are having trouble with the 
> first step of uploading files. The only thing that will currently upload is 
> text pasted into the URL/Text box.
>  
> Any attempt to upload a file using the Browse File box not only fails, it 
> never even starts. It's as if the Execute button is disabled.
>  
> I've tried changing the ajax-upload parameter to "false" in 
> tools/data_source/upload.xml (as mentioned in a workaround posted to the list 
> by Daniel Blankenburg in Aug 2012). I've also tried using different browsers 
> (including Internet Explorer) and going the route of Adding Data Libraries as 
> Admin. None of those attempts have worked.
>  
> Am I missing a configuration setup? Could there be permissions issues on the 
> Galaxy machine?
>  
> Thanks.
>  
> Steve
>  
> ___
> 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/

--- Begin Message ---
We've also seen that same error in our startup log:

==

Traceback (most recent call last):
  File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py",
line 447, in _load_plugin
module = __import__( module_name )
  File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py",
line 232
worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ),
target=self.run_next )
 ^
SyntaxError: invalid syntax

===

And we are also having trouble uploading files. Originally, even attempts to 
add files via the Admin Data Libraries process wouldn't work. That seems to 
have been resolved (coincidentally? or causally?) after another user completed 
a general upload via a URL.

But even now, uploading a specific file with the Get Data -> Upload File 
process is still non-responsive. Either the Execute button never does anything 
at all, or the upload process appears in History and turns blue but never 
completes.


-Original Message-
From: Dan Tenenbaum [mailto:dtene...@fhcrc.org]
Sent: Friday, February 01, 2013 3:14 PM
To: Stephen Groenewold
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] File Upload doesn't generate any activity

On Fri, Feb 1, 2013 at 8:41 AM, Stephen Groenewold  
wrote:
> We've  installed a local instance of Galaxy and are having trouble
> with the first step of uploading files. The only thing that will
> currently upload is text pasted into the URL/Text box.
>
>
>
> Any attempt to upload a file using the Browse File box not only fails,
> it never even starts. It's as if the Execute button is disabled.
>
>
>
> I've tried changing the ajax-upload parameter to "false" in
> tools/data_source/upload.xml (as mentioned in a workaround posted to
> the list by Daniel Blankenburg in Aug 2012). I've also tried using
> different browsers (including Internet Explorer) and going the route
> of Adding Data Libraries as Admin. None of those attempts have worked.
>
>
>
> Am I missing a configuration setup? Could there be permissions issues
> on the Galaxy machine?
>
>

This sounds like the same issue I've reported to this list, wh

Re: [galaxy-dev] Why "upload" to Local Instance rather than "import"?

[Dannon Baker]

The absolute fastest method would be to enable filepath upload for data 
libraries (in universe_wsgi.ini -- allow_library_path_paste = True).  Once 
that's set, you can paste the absolute file path into the upload box, and check 
the box for not copying the data.  This will leave the data where it is on the 
external drive, though it will make it available in the Data Library.  
Obviously if you use this method, you'll need to have that external drive 
attached (and always at the same mount point) to use the data.

If you actually *do* want to copy this data off the external drive, simply 
don't check that 'no copy' checkbox and the data will be copied directly 
through the filesystem and not uploaded.

-Dannon


On Feb 4, 2013, at 5:36 PM, "Thyssen, Gregory - ARS" 
 wrote:

> I have a local instance of Galaxy running on my workstation.
> I have external hard drives full of fastq sequencing files.
> I want to make them available to myself as data libraries.  I am the Admin 
> and sole user at this point.
> The “upload” data libraries seems to pass the data through the (slow) 
> network, even though my workstation and external hard drives are linked by 
> USB.
> What is the fastest way to import my files into my galaxy instance? Can I 
> copy them into some folder on the workstation’s hard drive?
> Since everything is physically connected, I don’t think I should be limited 
> by my network speed.
> Thanks,
> Greg Thyssen
>  
>  
> Gregory Thyssen, PhD
> Molecular Biologist
> Cotton Fiber Bioscience
> USDA-ARS-Southern Regional Research Center
> 1100 Robert E Lee Blvd
> New Orleans, LA 70124
> gregory.thys...@ars.usda.gov
> 504-286-4280
>  
>  
> 
> 
> 
> 
> This electronic message contains information generated by the USDA solely for 
> the intended recipients. Any unauthorized interception of this message or the 
> use or disclosure of the information it contains may violate the law and 
> subject the violator to civil or criminal penalties. If you believe you have 
> received this message in error, please notify the sender and delete the email 
> immediately. ___
> 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/


___
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/

[galaxy-dev] Why "upload" to Local Instance rather than "import"?

[Thyssen, Gregory - ARS]

I have a local instance of Galaxy running on my workstation.
I have external hard drives full of fastq sequencing files.
I want to make them available to myself as data libraries.  I am the Admin and 
sole user at this point.
The "upload" data libraries seems to pass the data through the (slow) network, 
even though my workstation and external hard drives are linked by USB.
What is the fastest way to import my files into my galaxy instance? Can I copy 
them into some folder on the workstation's hard drive?
Since everything is physically connected, I don't think I should be limited by 
my network speed.
Thanks,
Greg Thyssen


Gregory Thyssen, PhD
Molecular Biologist
Cotton Fiber Bioscience
USDA-ARS-Southern Regional Research Center
1100 Robert E Lee Blvd
New Orleans, LA 70124
gregory.thys...@ars.usda.gov
504-286-4280






This electronic message contains information generated by the USDA solely for 
the intended recipients. Any unauthorized interception of this message or the 
use or disclosure of the information it contains may violate the law and 
subject the violator to civil or criminal penalties. If you believe you have 
received this message in error, please notify the sender and delete the email 
immediately.
___
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/

[galaxy-dev] Changing job command line.

[James Boocock]

Hi All,

I am currently working on a clustering interface for galaxy that will
hopefully enable users to pick the grid
in the tool form.

With tools that need access to files within the galaxy directory, I
have an idea to create a symlinked
fake galaxy root with all the files the tools needs for galaxy. This
is done currently in my own xml format
for each grid.

Problem is when parsing a tool_wrapper variable I need to prepare the
job and add my additional commands
to the command line so that the fake galaxy dir is created with the
symlinked databases.

Is it bad practice to disable preparation in each tool runner if the
job has come from my clustering module
or is there a better way to do this. Will the job runners
wrapper.prepare() overwrite any of my changes to the command-line
when the job makes its way to the runner say local.py.


Cheers James.
___
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/

Re: [galaxy-dev] Local toolshed not working "HTTPError: HTTP Error 400: Bad Request"

[Greg Von Kuster]

Thanks for the information Carlos, I'll add this to the tool shed wiki.

On Feb 4, 2013, at 5:19 PM, Carlos Borroto wrote:

> Solved!
> 
> It was related to my proxy configuration after all. Setting the
> no_proxy environment variable fixed this issue for me. I see this is a
> corner case but just in case someone else runs into it, this is a
> summary of what I did.
> 
> If your network uses a http proxy who do not answer to local hostnames
> requests and you have setup the http_proxy environment variable. In
> order to get a local toolshed going, you will need to do two things.
> 
> - Add to ~/.hgrc:
> [http_proxy]
> no = [comma separated list of hostnames for your local toolsheds.
> Note: domain regex won't work]
> 
> - Set no_proxy environment variable. For bash in Redhat/CentOS I like
> adding to /etc/profile.d/custom.sh:
> export no_proxy=[comma separated list of local domains]
> 
> Hope it helps,
> Carlos
> ___
> 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/

___
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/

Re: [galaxy-dev] Local toolshed not working "HTTPError: HTTP Error 400: Bad Request"

[Carlos Borroto]

Solved!

It was related to my proxy configuration after all. Setting the
no_proxy environment variable fixed this issue for me. I see this is a
corner case but just in case someone else runs into it, this is a
summary of what I did.

If your network uses a http proxy who do not answer to local hostnames
requests and you have setup the http_proxy environment variable. In
order to get a local toolshed going, you will need to do two things.

- Add to ~/.hgrc:
[http_proxy]
no = [comma separated list of hostnames for your local toolsheds.
Note: domain regex won't work]

- Set no_proxy environment variable. For bash in Redhat/CentOS I like
adding to /etc/profile.d/custom.sh:
export no_proxy=[comma separated list of local domains]

Hope it helps,
Carlos
___
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/

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

[Carl Eberhard]

Even better - thanks again, Carlos - and thanks for the help in tracking
this down, Dan.


On Mon, Feb 4, 2013 at 4:46 PM, Dan Tenenbaum  wrote:

> On Mon, Feb 4, 2013 at 1:21 PM, Carl Eberhard 
> wrote:
> > Just to be clear, Dan - this solved the login issue and not the upload
> issue
> > (in which case I'd owe Carlos a six-pack), correct?
>
> Sorry...this solved both issues.
> Dan
>
>
> > C
> >
> >
> > On Mon, Feb 4, 2013 at 4:04 PM, Carl Eberhard 
> > wrote:
> >>
> >> Thanks much, Carlos - I owe you a beer!
> >>
> >>
> >> On Mon, Feb 4, 2013 at 4:01 PM, Dan Tenenbaum 
> wrote:
> >>>
> >>> On Mon, Feb 4, 2013 at 11:45 AM, Carlos Borroto
> >>>  wrote:
> >>> > On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum 
> >>> > wrote:
> >>> >>> Re: login: I believe there's a redirect in place that moves you
> past
> >>> >>> the
> >>> >>> older 'Return to the homepage' message automatically - I think
> you're
> >>> >>> good
> >>> >>> there (and logged in). Are you seeing the 'Logged in as  email>'
> >>> >>> in the
> >>> >>> 'User' menu at the top?
> >>> >>>
> >>> >>
> >>> >> No. I think I'm not actually being logged in.
> >>> >> All I see under the User menu is "Login" and "Register".
> >>> >
> >>> > I realize this is a long thread and my recommendation might not help
> >>> > much or was done it already. Sorry if that's the case.
> >>> >
> >>> > This behavior is something I have seen often with Chrome in
> particular
> >>> > and 99% of the time is related to an old cookie. Specially when I'm
> >>> > accessing a different galaxy instance from the same URL I accessed a
> >>> > previous one, something I see Dan did at the beginning of this
> thread.
> >>> > I recommend erasing any cookie related to galaxy and also trying with
> >>> > a different browser. Firefox seems to work particularly fine.
> >>> >
> >>>
> >>> Indeed, it works with Firefox. And it works with Chrome after I delete
> >>> my cookies.
> >>>
> >>> Thanks very much!
> >>> Dan
> >>>
> >>>
> >>> > Hope it helps,
> >>> > Carlos
> >>
> >>
> >
>
___
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/

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

[Carlos Borroto]

On Mon, Feb 4, 2013 at 4:46 PM, Dan Tenenbaum  wrote:
> On Mon, Feb 4, 2013 at 1:21 PM, Carl Eberhard  wrote:
>> Just to be clear, Dan - this solved the login issue and not the upload issue
>> (in which case I'd owe Carlos a six-pack), correct?
>
> Sorry...this solved both issues.

Great, glad it helped. Carl I like Sam Adams ;-).
___
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/

Re: [galaxy-dev] Local toolshed not working "HTTPError: HTTP Error 400: Bad Request"

[Carlos Borroto]

On Mon, Feb 4, 2013 at 2:01 PM, Carlos Borroto  wrote:
> I can manually confirm this URL is incorrect:
> tool_shed_url=http://toolsheddev.bfx.brel.local:9009/&repository_ids=ee9b707789bf4714&changeset_revisions=71b062907e0d
>
> When I try to directly access it I get this error:
> Not Found
>
> The resource could not be found.
> No action for 
> /&repository_ids=ee9b707789bf4714&changeset_revisions=71b062907e0d

Well after some more testing it seems this is not correct. I checked
what happens when I'm installing a tool from the Galaxy's main
toolshed and I get a similar behavior.

Galaxy's main toolshed:
[04/Feb/2013:16:40:31 -0400] "GET
/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=a23b0627623c
HTTP/1.1" 200 -
"http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=1d92ebdf7e8d466c&changeset_revision=a23b0627623c";
"Mozilla/5.0 (Windows NT 6.1; WOW64; rv:18.0) Gecko/20100101
Firefox/18.0"

This URL also cannot be accessed directly but that doesn't stops the
tool from being correctly installed:
tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=a23b0627623c

Local toolshed:
[04/Feb/2013:16:41:53 -0400] "GET
/admin_toolshed/prepare_for_install?tool_shed_url=http://toolsheddev.bfx.brel.local:9009/&repository_ids=ee9b707789bf4714&changeset_revisions=38d24f5c5bae
HTTP/1.1" 500 -
"http://toolsheddev.bfx.brel.local:9009/repository/preview_tools_in_changeset?repository_id=ee9b707789bf4714&changeset_revision=38d24f5c5bae";
"Mozilla/5.0 (Windows NT 6.1; WOW64; rv:18.0) Gecko/20100101
Firefox/18.0"

What I do see is "HTTP/1.1 200" response from Galaxy's main and
"HTTP/1.1 500" from my local toolshed. I'll keep pocking around to see
what I can find.

--Carlos
___
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/

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

[Dan Tenenbaum]

On Mon, Feb 4, 2013 at 1:21 PM, Carl Eberhard  wrote:
> Just to be clear, Dan - this solved the login issue and not the upload issue
> (in which case I'd owe Carlos a six-pack), correct?

Sorry...this solved both issues.
Dan


> C
>
>
> On Mon, Feb 4, 2013 at 4:04 PM, Carl Eberhard 
> wrote:
>>
>> Thanks much, Carlos - I owe you a beer!
>>
>>
>> On Mon, Feb 4, 2013 at 4:01 PM, Dan Tenenbaum  wrote:
>>>
>>> On Mon, Feb 4, 2013 at 11:45 AM, Carlos Borroto
>>>  wrote:
>>> > On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum 
>>> > wrote:
>>> >>> Re: login: I believe there's a redirect in place that moves you past
>>> >>> the
>>> >>> older 'Return to the homepage' message automatically - I think you're
>>> >>> good
>>> >>> there (and logged in). Are you seeing the 'Logged in as '
>>> >>> in the
>>> >>> 'User' menu at the top?
>>> >>>
>>> >>
>>> >> No. I think I'm not actually being logged in.
>>> >> All I see under the User menu is "Login" and "Register".
>>> >
>>> > I realize this is a long thread and my recommendation might not help
>>> > much or was done it already. Sorry if that's the case.
>>> >
>>> > This behavior is something I have seen often with Chrome in particular
>>> > and 99% of the time is related to an old cookie. Specially when I'm
>>> > accessing a different galaxy instance from the same URL I accessed a
>>> > previous one, something I see Dan did at the beginning of this thread.
>>> > I recommend erasing any cookie related to galaxy and also trying with
>>> > a different browser. Firefox seems to work particularly fine.
>>> >
>>>
>>> Indeed, it works with Firefox. And it works with Chrome after I delete
>>> my cookies.
>>>
>>> Thanks very much!
>>> Dan
>>>
>>>
>>> > Hope it helps,
>>> > Carlos
>>
>>
>
___
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/

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

[Carl Eberhard]

Just to be clear, Dan - this solved the login issue and not the upload
issue (in which case I'd owe Carlos a six-pack), correct?
C


On Mon, Feb 4, 2013 at 4:04 PM, Carl Eberhard wrote:

> Thanks much, Carlos - I owe you a beer!
>
>
> On Mon, Feb 4, 2013 at 4:01 PM, Dan Tenenbaum  wrote:
>
>> On Mon, Feb 4, 2013 at 11:45 AM, Carlos Borroto
>>  wrote:
>> > On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum 
>> wrote:
>> >>> Re: login: I believe there's a redirect in place that moves you past
>> the
>> >>> older 'Return to the homepage' message automatically - I think you're
>> good
>> >>> there (and logged in). Are you seeing the 'Logged in as '
>> in the
>> >>> 'User' menu at the top?
>> >>>
>> >>
>> >> No. I think I'm not actually being logged in.
>> >> All I see under the User menu is "Login" and "Register".
>> >
>> > I realize this is a long thread and my recommendation might not help
>> > much or was done it already. Sorry if that's the case.
>> >
>> > This behavior is something I have seen often with Chrome in particular
>> > and 99% of the time is related to an old cookie. Specially when I'm
>> > accessing a different galaxy instance from the same URL I accessed a
>> > previous one, something I see Dan did at the beginning of this thread.
>> > I recommend erasing any cookie related to galaxy and also trying with
>> > a different browser. Firefox seems to work particularly fine.
>> >
>>
>> Indeed, it works with Firefox. And it works with Chrome after I delete
>> my cookies.
>>
>> Thanks very much!
>> Dan
>>
>>
>> > Hope it helps,
>> > Carlos
>>
>
>
___
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/

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

[Dan Tenenbaum]

On Mon, Feb 4, 2013 at 11:45 AM, Carlos Borroto
 wrote:
> On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum  wrote:
>>> Re: login: I believe there's a redirect in place that moves you past the
>>> older 'Return to the homepage' message automatically - I think you're good
>>> there (and logged in). Are you seeing the 'Logged in as ' in the
>>> 'User' menu at the top?
>>>
>>
>> No. I think I'm not actually being logged in.
>> All I see under the User menu is "Login" and "Register".
>
> I realize this is a long thread and my recommendation might not help
> much or was done it already. Sorry if that's the case.
>
> This behavior is something I have seen often with Chrome in particular
> and 99% of the time is related to an old cookie. Specially when I'm
> accessing a different galaxy instance from the same URL I accessed a
> previous one, something I see Dan did at the beginning of this thread.
> I recommend erasing any cookie related to galaxy and also trying with
> a different browser. Firefox seems to work particularly fine.
>

Indeed, it works with Firefox. And it works with Chrome after I delete
my cookies.

Thanks very much!
Dan


> Hope it helps,
> Carlos
___
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/

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

[Carlos Borroto]

On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum  wrote:
>> Re: login: I believe there's a redirect in place that moves you past the
>> older 'Return to the homepage' message automatically - I think you're good
>> there (and logged in). Are you seeing the 'Logged in as ' in the
>> 'User' menu at the top?
>>
>
> No. I think I'm not actually being logged in.
> All I see under the User menu is "Login" and "Register".

I realize this is a long thread and my recommendation might not help
much or was done it already. Sorry if that's the case.

This behavior is something I have seen often with Chrome in particular
and 99% of the time is related to an old cookie. Specially when I'm
accessing a different galaxy instance from the same URL I accessed a
previous one, something I see Dan did at the beginning of this thread.
I recommend erasing any cookie related to galaxy and also trying with
a different browser. Firefox seems to work particularly fine.

Hope it helps,
Carlos
___
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/

Re: [galaxy-dev] psiblast

[Peter Cock]

On Monday, February 4, 2013, Luobin Yang wrote:

> Hi, Peter,
>
> Thanks for pointing them out!
>
> The phi-blast and psi-blast actually share the same binary, both use the
> psiblast program in the NCBI BLAST+ tools. When the option -phi_pattern is
> used, then it does phi-blast searching.
>
> Best,
> Luobin
>
>
>
Could you give a few command line examples of how you typically use
psiblast,  focussing in the main options only?

I would find that helpful when putting together a new wrapper - since
including all the options right away is overwhelming.

Thanks,

Peter
___
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/

[galaxy-dev] Local toolshed not working "HTTPError: HTTP Error 400: Bad Request"

[Carlos Borroto]

Hi,

I interested in hosting a local toolshed. I was able to install it and
add a tool to it. I have configured my local galaxy instance to pull
tools from this local toolshed. As far as I can tell everything is
working in the toolshed side of things, but when I try to install the
tool I added I get this error:

URL: 
http://galaxydev.bfx.brel.local/admin_toolshed/prepare_for_install?tool_shed_url=http://toolsheddev.bfx.brel.local:9009/&repository_ids=ee9b707789bf4714&changeset_revisions=71b062907e0d
File 
'/local/opt/galaxy/galaxy-dist.dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
  app_iter = self.application(environ, detect_start_response)
File 
'/local/opt/galaxy/galaxy-dist.dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py',
line 98 in __call__
  environ, self.app)
File 
'/local/opt/galaxy/galaxy-dist.dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py',
line 539 in intercept_output
  app_iter = application(environ, replacement_start_response)
File 
'/local/opt/galaxy/galaxy-dist.dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
line 80 in __call__
  return self.application(environ, start_response)
File 
'/local/opt/galaxy/galaxy-dist.dev/lib/galaxy/web/framework/middleware/remoteuser.py',
line 91 in __call__
  return self.app( environ, start_response )
File 
'/local/opt/galaxy/galaxy-dist.dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
line 632 in __call__
  return self.application(environ, start_response)
File '/local/opt/galaxy/galaxy-dist.dev/lib/galaxy/web/framework/base.py',
line 160 in __call__
  body = method( trans, **kwargs )
File '/local/opt/galaxy/galaxy-dist.dev/lib/galaxy/web/framework/__init__.py',
line 208 in decorator
  return func( self, trans, *args, **kwargs )
File 
'/local/opt/galaxy/galaxy-dist.dev/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
line 1177 in prepare_for_install
  response = urllib2.urlopen( url )
File '/usr/lib64/python2.6/urllib2.py', line 126 in urlopen
  return _opener.open(url, data, timeout)
File '/usr/lib64/python2.6/urllib2.py', line 397 in open
  response = meth(req, response)
File '/usr/lib64/python2.6/urllib2.py', line 510 in http_response
  'http', request, response, code, msg, hdrs)
File '/usr/lib64/python2.6/urllib2.py', line 435 in error
  return self._call_chain(*args)
File '/usr/lib64/python2.6/urllib2.py', line 369 in _call_chain
  result = func(*args)
File '/usr/lib64/python2.6/urllib2.py', line 518 in http_error_default
  raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
HTTPError: HTTP Error 400: Bad Request

I can manually confirm this URL is incorrect:
tool_shed_url=http://toolsheddev.bfx.brel.local:9009/&repository_ids=ee9b707789bf4714&changeset_revisions=71b062907e0d

When I try to directly access it I get this error:
Not Found

The resource could not be found.
No action for /&repository_ids=ee9b707789bf4714&changeset_revisions=71b062907e0d

I don't think is related but maybe I should mention it. I have to use
a http proxy to access the web, so I have http_proxy environment
variable set. This was causing issues with the local toolshed as my
institution proxy won't respond for requests to local hostnames. The
tool files would get uploaded but resetting the metadata would fail
with:
galaxy.util.shed_util_common DEBUG 2013-02-04 13:02:38,221 Resetting
all metadata on repository: annotab
galaxy.util.shed_util_common DEBUG 2013-02-04 13:02:38,271 Cloning
repository revision: 0
galaxy.util.shed_util_common DEBUG 2013-02-04 13:02:38,276 Error
cloning repository: HTTP Error 400: Bad Request
galaxy.util.shed_util_common DEBUG 2013-02-04 13:02:38,326 Cloning
repository revision: 1
galaxy.util.shed_util_common DEBUG 2013-02-04 13:02:38,329 Error
cloning repository: HTTP Error 400: Bad Request
galaxy.util.shed_util_common DEBUG 2013-02-04 13:02:38,377 Cloning
repository revision: 2
galaxy.util.shed_util_common DEBUG 2013-02-04 13:02:38,380 Error
cloning repository: HTTP Error 400: Bad Request

I was able to fix this issue by editing ~/.hgrc and adding:
[http_proxy]
no = toolshed.bfx.brel.local,toolsheddev.bfx.brel.local

I mention it just in case for some reason my issue could be related,
although as I said I don't think so.

Any help would be most welcomed,
Thanks,
Carlos
___
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/

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

[Carl Eberhard]

Sorry about the miscommunication: when I mentioned 'make sure you're using
a fresh history' I meant that you may want to go to the history options
menu (the gear in the upper right of the history panel and click 'Create
new'). It may be that previous datasets are causing some of the problems
we're seeing (and you wouldn't see deleted datasets - even though they are
still there - unless you checked the 'Include deleted datasets' from that
same history options menu).

Re: login: I believe there's a redirect in place that moves you past the
older 'Return to the homepage' message automatically - I think you're good
there (and logged in). Are you seeing the 'Logged in as ' in
the 'User' menu at the top?

Re: the error: so it looks like this is back to square one (the original
error). If this still happens after you've ensured you're using a new
history - I'll keep digging.
C


On Mon, Feb 4, 2013 at 1:30 PM, Dan Tenenbaum  wrote:

> Hi Carl,
>
> On Mon, Feb 4, 2013 at 10:22 AM, Carl Eberhard 
> wrote:
> > Hello, Dan.
> > I'm glad you updated.
> >
> > I noticed another error in your log:
> > 127.0.0.1 - - [04/Feb/2013:09:50:43 -0700] "POST
> > /tool_runner/upload_async_create HTTP/1.1" 500 - "http://localhost:8080/
> "
> > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17
> (KHTML,
> > like Gecko) Chrome/24.0.1312.57 Safari/537.17"
> > Debug at: http://localhost:8080/_debug/view/136104
> >
> > Two things -
> >
> > 1. Can you restart your daemon and make sure you're using a fresh history
> > before the upload?
>
> Not sure what you mean by this. I have no items in my history...
>
> > 2. If you're upload fails this time, would you search your paster.log for
> > something close to "Debug at: http://localhost:8080/_debug/view/";... and
> > navigate there with your browser? It should show that error in more depth
> > and allow you to post that here.
> >
>
> Here it is:
>
> URL: http://localhost:8080/tool_runner/upload_async_create
> File
> '/Users/dtenenba/dev/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py',
> line 364 in respond
>   app_iter = self.application(environ, detect_start_response)
> File
> '/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py',
> line 98 in __call__
>   environ, self.app)
> File
> '/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py',
> line 539 in intercept_output
>   app_iter = application(environ, replacement_start_response)
> File
> '/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py',
> line 80 in __call__
>   return self.application(environ, start_response)
> File
> '/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py',
> line 632 in __call__
>   return self.application(environ, start_response)
> File '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/web/framework/base.py',
> line 160 in __call__
>   body = method( trans, **kwargs )
> File
> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/web/framework/__init__.py',
> line 73 in decorator
>   return simplejson.dumps( func( self, trans, *args, **kwargs ) )
> File
> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
> line 317 in upload_async_create
>   datasets.append( create_dataset( name ) )
> File
> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
> line 287 in create_dataset
>   return upload_common.new_upload( trans, cntrller, ud,
> library_bunch=library_bunch,
> state=trans.app.model.HistoryDatasetAssociation.states.UPLOAD )
> File
> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/actions/upload_common.py',
> line 213 in new_upload
>   return new_history_upload( trans, uploaded_dataset, state )
> File
> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/actions/upload_common.py',
> line 118 in new_history_upload
>   hda.state = state
> File '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/model/__init__.py',
> line 1048 in set_dataset_state
>   object_session( self ).add( self.dataset )
> AttributeError: 'NoneType' object has no attribute 'add'
>
> I did try and log in. The green panel that says I have logged in
> flashed past for a split second.
>
> I'm attaching the latest paster.log again as well.
>
>
> Thanks,
> Dan
>
>
> > Thanks for the help,
> > C
> >
> >
> >
> >
> > On Mon, Feb 4, 2013 at 12:55 PM, Dan Tenenbaum 
> wrote:
> >>
> >> Hi Carl,
> >>
> >> On Thu, Jan 31, 2013 at 1:37 PM, Dan Tenenbaum 
> wrote:
> >> > Here you go. I notice a couple of stack traces.
> >> > Thanks!
> >> > Dan
> >> >
> >> >
> >>
> >> I noticed that another user on the list seemed to have a similar
> >> problem and I saw that that problem was possibly addressed in a new
> >> commit. I updated to 8531:3299529e0fe8 and I still have the same
> >> problem, but perhaps different output.
> >>
> >> I tried logging in and the UI does not seem to recognize that I have
> >> logged in. Then I tried to upload a file and it failed, with a
> >> tr

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

[Carl Eberhard]

Hello, Dan.
I'm glad you updated.

I noticed another error in your log:
127.0.0.1 - - [04/Feb/2013:09:50:43 -0700] "POST
/tool_runner/upload_async_create HTTP/1.1" 500 - "http://localhost:8080/";
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML,
like Gecko) Chrome/24.0.1312.57 Safari/537.17"
Debug at: http://localhost:8080/_debug/view/136104

Two things -

1. Can you restart your daemon and make sure you're using a fresh history
before the upload?
2. If you're upload fails this time, would you search your paster.log for
something close to "Debug at: http://localhost:8080/_debug/view/";... and
navigate there with your browser? It should show that error in more depth
and allow you to post that here.

Thanks for the help,
C




On Mon, Feb 4, 2013 at 12:55 PM, Dan Tenenbaum  wrote:

> Hi Carl,
>
> On Thu, Jan 31, 2013 at 1:37 PM, Dan Tenenbaum  wrote:
> > Here you go. I notice a couple of stack traces.
> > Thanks!
> > Dan
> >
> >
>
> I noticed that another user on the list seemed to have a similar
> problem and I saw that that problem was possibly addressed in a new
> commit. I updated to 8531:3299529e0fe8 and I still have the same
> problem, but perhaps different output.
>
> I tried logging in and the UI does not seem to recognize that I have
> logged in. Then I tried to upload a file and it failed, with a
> traceback in the console:
>
> 127.0.0.1 - - [04/Feb/2013:09:45:13 -0700] "GET /history HTTP/1.1" 200
> - "http://localhost:8080/tool_runner/index"; "Mozilla/5.0 (Macintosh;
> Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko)
> Chrome/24.0.1312.57 Safari/537.17"
> 127.0.0.1 - - [04/Feb/2013:09:45:12 -0700] "GET /history HTTP/1.1" 200
> - "http://localhost:8080/tool_runner/upload_async_message";
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17
> (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17"
> 
> Exception happened during processing of request from ('127.0.0.1', 49617)
> Traceback (most recent call last):
>   File
> "/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
> line 1053, in process_request_in_thread
> self.finish_request(request, client_address)
>   File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py",
> line 323, in finish_request
> self.RequestHandlerClass(request, client_address, self)
>   File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py",
> line 641, in __init__
> self.finish()
>   File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py",
> line 694, in finish
> self.wfile.flush()
>   File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py",
> line 303, in flush
> self._sock.sendall(view[write_offset:write_offset+buffer_size])
> error: [Errno 32] Broken pipe
> 
>
> Then I started a daemon session in order to be able to send you the
> full output, but, although the upload still fails, I don't get this
> same traceback in the paster.log. I attach it anyway.
>
> Thanks,
> Dan
>
>
>
> > On Thu, Jan 31, 2013 at 12:15 PM, Carl Eberhard 
> wrote:
> >> Ok - interesting!
> >> Can you send me the paster.log from a daemon session where you try an
> >> upload?
> >>
> >> Steps for that are:
> >> 1. from the directory of your galaxy installation: sh run.sh --daemon
> (you
> >> should see 'Entering daemon mode')
> >> 2. Wait a minute, then load localhost:8080 in your browser, login, and
> try
> >> an upload
> >> 3. When that fails, you can shut down: (from the galaxy installation
> again)
> >> sh run.sh --stop-daemon
> >>
> >> The file 'paster.log' should be in that same directory.
> >>
> >> Let me know if there are any problems,
> >> C
> >>
> >>
>
___
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/

Re: [galaxy-dev] psiblast

[Luobin Yang]

Hi, Peter,

Thanks for pointing them out!

The phi-blast and psi-blast actually share the same binary, both use the
psiblast program in the NCBI BLAST+ tools. When the option -phi_pattern is
used, then it does phi-blast searching.

Best,
Luobin

On Mon, Feb 4, 2013 at 11:14 AM, Peter Cock wrote:

> On Mon, Feb 4, 2013 at 5:43 PM, Luobin Yang  wrote:
> > Hi, Peter,
> >
> > What difficulties did you see to include psi-blast and phi-blast when you
> > were working on the other programs in the NCBI+ suite? I would be
> interested
> > in creating a tool configuration file for each of these two.
> >
> > Thanks,
> > Luobin
>
> Hi Luobin,
>
> At first glance, the binaries for psiblast, rpsblast, and rpstblastn don't
> look too different for wrapping. We would need to define a third loc
> file for the RPS BLAST domain databases (like the existing loc files
> for nucleotide and protein databases).
>
> However, I'm not immediately sure where phi-blast existing with the
> standalone NCBI BLAST+ tools. Do you know?
>
> Peter
>
___
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/

Re: [galaxy-dev] psiblast

[Peter Cock]

On Mon, Feb 4, 2013 at 5:43 PM, Luobin Yang  wrote:
> Hi, Peter,
>
> What difficulties did you see to include psi-blast and phi-blast when you
> were working on the other programs in the NCBI+ suite? I would be interested
> in creating a tool configuration file for each of these two.
>
> Thanks,
> Luobin

Hi Luobin,

At first glance, the binaries for psiblast, rpsblast, and rpstblastn don't
look too different for wrapping. We would need to define a third loc
file for the RPS BLAST domain databases (like the existing loc files
for nucleotide and protein databases).

However, I'm not immediately sure where phi-blast existing with the
standalone NCBI BLAST+ tools. Do you know?

Peter
___
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/

Re: [galaxy-dev] File Upload doesn't generate any activity

[Nicola Soranzo]

Il giorno lun, 04/02/2013 alle 17.41 +, Hakeem Almabrazi ha
scritto: 
> Thank you Nicola,
> 
> Should I replace my current galaxy-dist with this version or is there 
> different way to upgrade?

Take a look at this wiki page:

http://wiki.galaxyproject.org/Admin/Get%
20Galaxy#Keep_your_code_up_to_date

Nicola

> -Original Message-
> From: Nicola Soranzo [mailto:sora...@crs4.it] 
> Sent: Monday, February 04, 2013 10:50 AM
> To: Hakeem Almabrazi
> Cc: Dannon Baker; Galaxy Dev
> Subject: Re: [galaxy-dev] File Upload doesn't generate any activity
> 
> Il giorno lun, 04/02/2013 alle 16.33 +, Hakeem Almabrazi ha
> scritto: 
> > Thank you Dannon.  Hopefully things should be moving forward from now on.
> > 
> > "This issue with the LWR has been fixed in changeset 8731:3299529e0fe8 
> > which will be in the next distribution release."
> > 
> > That will be awesome.
> 
> It's already in galaxy-dist since Saturday 2013/02/02, changeset
> 8531:3299529e0fe8 .
> 
> Kind Regards,
> Nicola
> 


___
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/

Re: [galaxy-dev] File Upload doesn't generate any activity

[Dannon Baker]

Thanks Nicola for reminding me that we'd already applied that changeset!

Hakeem, you should be able to simply 'hg pull -u' from your galaxy-dist 
directory and then restart galaxy with the changes applied.

-Dannon


On Feb 4, 2013, at 12:41 PM, Hakeem Almabrazi  wrote:

> Thank you Nicola,
> 
> Should I replace my current galaxy-dist with this version or is there 
> different way to upgrade?
> 
> Thank you...
> 
> -Original Message-
> From: Nicola Soranzo [mailto:sora...@crs4.it] 
> Sent: Monday, February 04, 2013 10:50 AM
> To: Hakeem Almabrazi
> Cc: Dannon Baker; Galaxy Dev
> Subject: Re: [galaxy-dev] File Upload doesn't generate any activity
> 
> Il giorno lun, 04/02/2013 alle 16.33 +, Hakeem Almabrazi ha
> scritto: 
>> Thank you Dannon.  Hopefully things should be moving forward from now on.
>> 
>> "This issue with the LWR has been fixed in changeset 8731:3299529e0fe8 which 
>> will be in the next distribution release."
>> 
>> That will be awesome.
> 
> It's already in galaxy-dist since Saturday 2013/02/02, changeset
> 8531:3299529e0fe8 .
> 
> Kind Regards,
> Nicola
> 
> -- 
> Nicola Soranzo, Ph.D.
> CRS4
> Bioinformatics Program
> Loc. Piscina Manna
> 09010 Pula (CA), Italy
> http://www.bioinformatica.crs4.it/
> 
>> -Original Message-
>> From: Dannon Baker [mailto:dannonba...@me.com] 
>> Sent: Monday, February 04, 2013 9:40 AM
>> To: Hakeem Almabrazi
>> Cc: Galaxy Dev
>> Subject: Re: [galaxy-dev] File Upload doesn't generate any activity
>> 
>> On Feb 4, 2013, at 10:36 AM, Hakeem Almabrazi  wrote:
>>> No there was nothing special about this installation.  I installed it on 
>>> CentOS and I tried to follow instructions in installing and configuring 
>>> tools and data.  The only thing that I did not was to test this feature 
>>> before I integrate it with postgres, nginx, tools such as bwa, samtools, 
>>> bowtie etc.  I might have done something not right while doing so.  But 
>>> once I was done with all the configuration steps, I tried to load files via 
>>> "Get Data" or "Data Library".  It kept spinning and nothing is actually 
>>> being written to the system.  I tailed the logs and it was writing some 
>>> logs every seconds but no errors or warnings.  
>>> 
>>> The issue was resolved when I used "URL/Text" to go to this link as another 
>>> trail test.  After that everything works just fine.  Now we can load files 
>>> via either way.
>> 
>> Very strange, but I'm glad it's working for you now.  If this does crop up 
>> again, let me know and we can try to reproduce what's happening and fix it.
>> 
>>> The only error I keep seeing in the log is when we restart the server and 
>>> from what I read, this is a bug...
>>> 
>>> Traceback (most recent call last):
>>> File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py",
>>> line 447, in _load_plugin
>>>   module = __import__( module_name )
>>> File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py",
>>> line 232
>>>   worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), 
>>> target=self.run_next )
>>>^
>>> SyntaxError: invalid syntax
>>> 
>>> 
>>> 
>>> Please let me know if you want me to do anything else that might help 
>>> debugging this issue.
> 
> 

___
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/

Re: [galaxy-dev] psiblast

[Luobin Yang]

Hi, Peter,

What difficulties did you see to include psi-blast and phi-blast when you
were working on the other programs in the NCBI+ suite? I would be
interested in creating a tool configuration file for each of these two.

Thanks,
Luobin

On Mon, Feb 4, 2013 at 10:30 AM, Peter Cock wrote:

> On Mon, Feb 4, 2013 at 5:20 PM, Luobin Yang  wrote:
> > Hi, Galaxy developers,
> >
> > I do not see a web interface for psi-blast in NCBI BLAST+ in the tool
> shed.
> > Does it have one?
> >
> > Thanks,
> > Luobin
>
> If you are asking about the ncbi_blast_plus suite in the Tool Shed, this
> has most of the key NCBI BLAST+ standalone tools now, but not yet
> psiblast or rpsblast.
>
> Peter
>
> P.S. When you said web-interface, did you mean to the NCBI online
> server? As far as I know there are no Galaxy interfaces to that - just
> for the standalone NCBI command line tools.
>
___
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/

Re: [galaxy-dev] File Upload doesn't generate any activity

[Hakeem Almabrazi]

Thank you Nicola,

Should I replace my current galaxy-dist with this version or is there different 
way to upgrade?

Thank you...

-Original Message-
From: Nicola Soranzo [mailto:sora...@crs4.it] 
Sent: Monday, February 04, 2013 10:50 AM
To: Hakeem Almabrazi
Cc: Dannon Baker; Galaxy Dev
Subject: Re: [galaxy-dev] File Upload doesn't generate any activity

Il giorno lun, 04/02/2013 alle 16.33 +, Hakeem Almabrazi ha
scritto: 
> Thank you Dannon.  Hopefully things should be moving forward from now on.
> 
> "This issue with the LWR has been fixed in changeset 8731:3299529e0fe8 which 
> will be in the next distribution release."
> 
> That will be awesome.

It's already in galaxy-dist since Saturday 2013/02/02, changeset
8531:3299529e0fe8 .

Kind Regards,
Nicola

-- 
Nicola Soranzo, Ph.D.
CRS4
Bioinformatics Program
Loc. Piscina Manna
09010 Pula (CA), Italy
http://www.bioinformatica.crs4.it/

> -Original Message-
> From: Dannon Baker [mailto:dannonba...@me.com] 
> Sent: Monday, February 04, 2013 9:40 AM
> To: Hakeem Almabrazi
> Cc: Galaxy Dev
> Subject: Re: [galaxy-dev] File Upload doesn't generate any activity
> 
> On Feb 4, 2013, at 10:36 AM, Hakeem Almabrazi  wrote:
> > No there was nothing special about this installation.  I installed it on 
> > CentOS and I tried to follow instructions in installing and configuring 
> > tools and data.  The only thing that I did not was to test this feature 
> > before I integrate it with postgres, nginx, tools such as bwa, samtools, 
> > bowtie etc.  I might have done something not right while doing so.  But 
> > once I was done with all the configuration steps, I tried to load files via 
> > "Get Data" or "Data Library".  It kept spinning and nothing is actually 
> > being written to the system.  I tailed the logs and it was writing some 
> > logs every seconds but no errors or warnings.  
> > 
> > The issue was resolved when I used "URL/Text" to go to this link as another 
> > trail test.  After that everything works just fine.  Now we can load files 
> > via either way.
> 
> Very strange, but I'm glad it's working for you now.  If this does crop up 
> again, let me know and we can try to reproduce what's happening and fix it.
> 
> > The only error I keep seeing in the log is when we restart the server and 
> > from what I read, this is a bug...
> > 
> > Traceback (most recent call last):
> >  File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py",
> > line 447, in _load_plugin
> >module = __import__( module_name )
> >  File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py",
> > line 232
> >worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), 
> > target=self.run_next )
> > ^
> > SyntaxError: invalid syntax
> > 
> > 
> > 
> > Please let me know if you want me to do anything else that might help 
> > debugging this issue.



___
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/

Re: [galaxy-dev] psiblast

[Luobin Yang]

Hi, Peter,

I mean the web interface for psiblast on Galaxy system, not the web
interface at NCBI.

Thanks,
Luobin

On Mon, Feb 4, 2013 at 10:30 AM, Peter Cock wrote:

> On Mon, Feb 4, 2013 at 5:20 PM, Luobin Yang  wrote:
> > Hi, Galaxy developers,
> >
> > I do not see a web interface for psi-blast in NCBI BLAST+ in the tool
> shed.
> > Does it have one?
> >
> > Thanks,
> > Luobin
>
> If you are asking about the ncbi_blast_plus suite in the Tool Shed, this
> has most of the key NCBI BLAST+ standalone tools now, but not yet
> psiblast or rpsblast.
>
> Peter
>
> P.S. When you said web-interface, did you mean to the NCBI online
> server? As far as I know there are no Galaxy interfaces to that - just
> for the standalone NCBI command line tools.
>
___
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/

Re: [galaxy-dev] psiblast

[Peter Cock]

On Mon, Feb 4, 2013 at 5:20 PM, Luobin Yang  wrote:
> Hi, Galaxy developers,
>
> I do not see a web interface for psi-blast in NCBI BLAST+ in the tool shed.
> Does it have one?
>
> Thanks,
> Luobin

If you are asking about the ncbi_blast_plus suite in the Tool Shed, this
has most of the key NCBI BLAST+ standalone tools now, but not yet
psiblast or rpsblast.

Peter

P.S. When you said web-interface, did you mean to the NCBI online
server? As far as I know there are no Galaxy interfaces to that - just
for the standalone NCBI command line tools.
___
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/

[galaxy-dev] psiblast

[Luobin Yang]

Hi, Galaxy developers,

I do not see a web interface for psi-blast in NCBI BLAST+ in the tool shed.
Does it have one?

Thanks,
Luobin
___
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/

Re: [galaxy-dev] File Upload doesn't generate any activity

[Nicola Soranzo]

Il giorno lun, 04/02/2013 alle 16.33 +, Hakeem Almabrazi ha
scritto: 
> Thank you Dannon.  Hopefully things should be moving forward from now on.
> 
> "This issue with the LWR has been fixed in changeset 8731:3299529e0fe8 which 
> will be in the next distribution release."
> 
> That will be awesome.

It's already in galaxy-dist since Saturday 2013/02/02, changeset
8531:3299529e0fe8 .

Kind Regards,
Nicola

-- 
Nicola Soranzo, Ph.D.
CRS4
Bioinformatics Program
Loc. Piscina Manna
09010 Pula (CA), Italy
http://www.bioinformatica.crs4.it/

> -Original Message-
> From: Dannon Baker [mailto:dannonba...@me.com] 
> Sent: Monday, February 04, 2013 9:40 AM
> To: Hakeem Almabrazi
> Cc: Galaxy Dev
> Subject: Re: [galaxy-dev] File Upload doesn't generate any activity
> 
> On Feb 4, 2013, at 10:36 AM, Hakeem Almabrazi  wrote:
> > No there was nothing special about this installation.  I installed it on 
> > CentOS and I tried to follow instructions in installing and configuring 
> > tools and data.  The only thing that I did not was to test this feature 
> > before I integrate it with postgres, nginx, tools such as bwa, samtools, 
> > bowtie etc.  I might have done something not right while doing so.  But 
> > once I was done with all the configuration steps, I tried to load files via 
> > "Get Data" or "Data Library".  It kept spinning and nothing is actually 
> > being written to the system.  I tailed the logs and it was writing some 
> > logs every seconds but no errors or warnings.  
> > 
> > The issue was resolved when I used "URL/Text" to go to this link as another 
> > trail test.  After that everything works just fine.  Now we can load files 
> > via either way.
> 
> Very strange, but I'm glad it's working for you now.  If this does crop up 
> again, let me know and we can try to reproduce what's happening and fix it.
> 
> > The only error I keep seeing in the log is when we restart the server and 
> > from what I read, this is a bug...
> > 
> > Traceback (most recent call last):
> >  File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py",
> > line 447, in _load_plugin
> >module = __import__( module_name )
> >  File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py",
> > line 232
> >worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), 
> > target=self.run_next )
> > ^
> > SyntaxError: invalid syntax
> > 
> > 
> > 
> > Please let me know if you want me to do anything else that might help 
> > debugging this issue.


___
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/

Re: [galaxy-dev] File Upload doesn't generate any activity

[Hakeem Almabrazi]

Thank you Dannon.  Hopefully things should be moving forward from now on.

"This issue with the LWR has been fixed in changeset 8731:3299529e0fe8 which 
will be in the next distribution release."

That will be awesome.

Regards,
 




-Original Message-
From: Dannon Baker [mailto:dannonba...@me.com] 
Sent: Monday, February 04, 2013 9:40 AM
To: Hakeem Almabrazi
Cc: Galaxy Dev
Subject: Re: [galaxy-dev] File Upload doesn't generate any activity

On Feb 4, 2013, at 10:36 AM, Hakeem Almabrazi  wrote:
> No there was nothing special about this installation.  I installed it on 
> CentOS and I tried to follow instructions in installing and configuring tools 
> and data.  The only thing that I did not was to test this feature before I 
> integrate it with postgres, nginx, tools such as bwa, samtools, bowtie etc.  
> I might have done something not right while doing so.  But once I was done 
> with all the configuration steps, I tried to load files via "Get Data" or 
> "Data Library".  It kept spinning and nothing is actually being written to 
> the system.  I tailed the logs and it was writing some logs every seconds but 
> no errors or warnings.  
> 
> The issue was resolved when I used "URL/Text" to go to this link as another 
> trail test.  After that everything works just fine.  Now we can load files 
> via either way.

Very strange, but I'm glad it's working for you now.  If this does crop up 
again, let me know and we can try to reproduce what's happening and fix it.

> The only error I keep seeing in the log is when we restart the server and 
> from what I read, this is a bug...
> 
> Traceback (most recent call last):
>  File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py",
> line 447, in _load_plugin
>module = __import__( module_name )
>  File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py",
> line 232
>worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), 
> target=self.run_next )
> ^
> SyntaxError: invalid syntax
> 
> 
> 
> Please let me know if you want me to do anything else that might help 
> debugging this issue.

This issue with the LWR has been fixed in changeset 8731:3299529e0fe8 which 
will be in the next distribution release.

-Dannon

___
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/

Re: [galaxy-dev] Toolshed tools minimal requirments for submission

[Greg Von Kuster]

Hi Alex,


On Feb 4, 2013, at 10:35 AM, Bossers, Alex wrote:

> Greg and Björn, thanks for the info.
>  
> I will again review that section. Indeed a simple tool just required an xml, 
> tool script and some README. But as you guessed I was more interested in 
> complexer types; One might be the use of a bowtie2 multi mapper script we use 
> to map fastq reads to a set of databases picked from the available bowtie 
> indices within galaxy. Graphs are generated with R.
>  
> So of course the xml and wrapper scripts should be there as well as the R 
> scripts.


R scripts are defined as tool dependencies that are contained within the same 
repository.
See 
http://wiki.galaxyproject.org/ToolShedToolFeatures#Finding_dependencies_included_in_an_installed_repository_at_tool_execution_time


> How about bowtie2_db.lock additions?


This is defined as a 3rd-party tool dependency, and you can include a file 
named tool_dependencies.xml that defines how to install and compile it and 
ensure your appropriate repository tool can locate the compiled dependency.
See 
http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories


> How to secure R and bowtie2? Just by requirements?

Can you clarify this question?


> And their licenses?

See http://wiki.galaxyproject.org/ToolShedReadmeFiles

>  
> Thanks
> Alex
>  
> Van: Greg Von Kuster [mailto:g...@bx.psu.edu] 
> Verzonden: maandag 4 februari 2013 16:25
> Aan: Bossers, Alex
> CC: galaxy-dev@lists.bx.psu.edu
> Onderwerp: Re: [galaxy-dev] Toolshed tools minimal requirments for submission
>  
> Hello Alex,
>  
> In very general terms, a repository should include everything necessary for 
> ensuring each if it's contained utilities is functionally correct when 
> installed into a local Galaxy instance.  Categories of Galaxy utilities are 
> Galaxy-specific tools, proprietary Galaxy datatypes, exported Galaxy 
> workflows, 3rd-party tool dependency definitions and repository dependency 
> definitions.
>  
> I believe the content of the original tool shed wiki is mostly retained in 
> the current wiki.  The original wiki was just divided into document sections, 
> and a lot of new content has been added because of the many new tool shed 
> features that have been introduced.  The main section detailing repository 
> content it is here:  
> http://wiki.galaxyproject.org/Tool%20Shed#The_contents_of_your_tool_shed_repository.
>   This page include many related pages whose links are at the bottom of the 
> page.
>  
> It is not possible to give a precise, but general definition of what should 
> be included in all repositories because repositories can contain different 
> types of Galaxy utilities.  Each of the sections of the wiki page link above 
> describes how to include these various Galaxy utilities.  
>  
> Even Galaxy tools fall into various categories.  For example, some are very 
> simple, requiring no 3rd party tool dependencies and the tool form does not 
> use dynamically generated select lists.  These generally only require a 
> script and an XML file.  However, more complex Galaxy tools may require 
> additional supporting content to be included in the repository (e.g., a 
> tool_data_table_conf.xml.sample file. etc)
>  
> If you could provide more details about what types of utilities you are 
> building, I can steer you to the wiki pages that provide information about 
> those specific utilities.  
>  
> Thanks!
>  
> Greg Von Kuster
>  
>  
> On Feb 4, 2013, at 9:53 AM, Bossers, Alex wrote:
> 
> 
> Hi All,
>  
> We are experimenting with local toolsheds for tool maintainability. On the 
> old galaxy wiki I can remember there was a short tutorial or small 
> description of the minimal requirements of a tool to be submitted to the 
> toolshed. Actually we submitted some.
> However we seem unable to retrieve the proper info from the updated wiki.
> We did find info on single tools or suites, or more special cases, but a 
> simple example/list of  how and what to include in a repository is missing 
> (at least we cannot find itmight be an issue of wrong key words)..
>  
> Anyone has an idea where to find such a document?
>  
> Thanks
> Alex
>  
>  
>  
> ___
> 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/
>  

___
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/

Re: [galaxy-dev] Toolshed tools minimal requirments for submission

[Björn Grüning]

Hi Alex,

for bowtie2 dependency have a look at the bismark wrapper in the main
toolshed [1]. For R please see that wiki page:

http://wiki.galaxyproject.org/ToolShedToolFeatures?highlight=%28script%
29

Happy hacking!
Bjoern



[1] hg clone http://toolshed.g2.bx.psu.edu/repos/bjoern-gruening/bismark



> Greg and Björn, thanks for the info.

> I will again review that section. Indeed a simple tool just required
> an xml, tool script and some README. But as you guessed I was more
> interested in complexer types; One might be the use of a bowtie2 multi
> mapper script we use to map fastq reads to a set of databases picked
> from the available bowtie indices within galaxy. Graphs are generated
> with R.
> 
>  
> 
> So of course the xml and wrapper scripts should be there as well as
> the R scripts.
> 
> How about bowtie2_db.lock additions?
> 
> How to secure R and bowtie2? Just by requirements?
> 
> And their licenses?
> 
>  
> 
> Thanks
> 
> Alex
> 
>  
> 
> Van: Greg Von Kuster [mailto:g...@bx.psu.edu] 
> Verzonden: maandag 4 februari 2013 16:25
> Aan: Bossers, Alex
> CC: galaxy-dev@lists.bx.psu.edu
> Onderwerp: Re: [galaxy-dev] Toolshed tools minimal requirments for
> submission
> 
> 
>  
> 
> Hello Alex,
> 
>  
> 
> 
> In very general terms, a repository should include everything
> necessary for ensuring each if it's contained utilities is
> functionally correct when installed into a local Galaxy instance.
>  Categories of Galaxy utilities are Galaxy-specific tools, proprietary
> Galaxy datatypes, exported Galaxy workflows, 3rd-party tool dependency
> definitions and repository dependency definitions.
> 
> 
>  
> 
> 
> I believe the content of the original tool shed wiki is mostly
> retained in the current wiki.  The original wiki was just divided into
> document sections, and a lot of new content has been added because of
> the many new tool shed features that have been introduced.  The main
> section detailing repository content it is here:
>  http://wiki.galaxyproject.org/Tool%
> 20Shed#The_contents_of_your_tool_shed_repository.  This page include
> many related pages whose links are at the bottom of the page.
> 
> 
>  
> 
> 
> It is not possible to give a precise, but general definition of what
> should be included in all repositories because repositories can
> contain different types of Galaxy utilities.  Each of the sections of
> the wiki page link above describes how to include these various Galaxy
> utilities.  
> 
> 
>  
> 
> 
> Even Galaxy tools fall into various categories.  For example, some are
> very simple, requiring no 3rd party tool dependencies and the tool
> form does not use dynamically generated select lists.  These generally
> only require a script and an XML file.  However, more complex Galaxy
> tools may require additional supporting content to be included in the
> repository (e.g., a tool_data_table_conf.xml.sample file. etc)
> 
> 
>  
> 
> 
> If you could provide more details about what types of utilities you
> are building, I can steer you to the wiki pages that provide
> information about those specific utilities.  
> 
> 
>  
> 
> 
> Thanks!
> 
> 
>  
> 
> 
> Greg Von Kuster
> 
> 
>  
> 
> 
>  
> 
> On Feb 4, 2013, at 9:53 AM, Bossers, Alex wrote:
> 
> 
> 
> 
> Hi All,
> 
> 
>  
> 
> 
> We are experimenting with local toolsheds for tool maintainability. On
> the old galaxy wiki I can remember there was a short tutorial or small
> description of the minimal requirements of a tool to be submitted to
> the toolshed. Actually we submitted some.
> 
> 
> However we seem unable to retrieve the proper info from the updated
> wiki.
> 
> 
> We did find info on single tools or suites, or more special cases, but
> a simple example/list of  how and what to include in a repository is
> missing (at least we cannot find itmight be an issue of wrong key
> words)..
> 
> 
>  
> 
> 
> Anyone has an idea where to find such a document?
> 
> 
>  
> 
> 
> Thanks
> 
> 
> Alex
> 
> 
>  
> 
> 
>  
> 
> 
>  
> 
> 
> ___
> 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/
> 
> 
>  
> 
> 
> ___
> 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/

-- 
Björn Grüning
Albert-Ludwigs-Universität Freiburg
Institute of Pharmaceutical Sciences
Pharmaceutical Bioinformatics
Hermann-Herder-Strasse 9
D-79104 Freiburg i. Br.

Tel.:  +49 761 203-4872
Fax.:  +49 761 203-97769
E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
Web: http://www.pharmaceutical-bioinformatics.org/

___
Please keep all replies on the list by using "reply all"
in your mail

Re: [galaxy-dev] Behaviour of download_by_url with tar.gz during tool dependency installation

[Greg Von Kuster]

Hello Jean-Frédéric,

Thanks very much for your wiki editing contributions - the particular page has 
been and continues to be on my list for making enhancements, and I'm currently 
planning on making some additions this week.

I apologize for the difference in how the extraction directories are determined 
for tar and zip archives.  The use of the target_filename attribute for tar 
archives is a recent enhancement that was required for migrating the lastz and 
bowtie tools from the Galaxy distribution, and I have not yet had a chance to 
update the wiki page accordingly (I will attempt to do so this week).

The tool_dependency.xml definitions have evolved enough that they are 
sufficient for defining the process for many 3rd party tool dependencies.  
However, they will continue to be refined as additional dependencies are 
discovered that cannot be installed using the current definitions.  I will 
continue to update the tool shed wiki page as these definition tag sets evolve.

Thanks very much for your message and your contributions.

Greg Von Kuster


On Jan 30, 2013, at 10:49 AM, Jean-Frédéric Berthelot wrote:

> Hi list,
> 
> When working to get a tool wrapper Toolshed-ready, I have explored how tool 
> dependencies installation works, especially the download_by_url feature.
> 
> I have summarised my understanding on the Wiki (hope this is clear and 
> accurate):
> 
> 
> The difference of behaviour when dealing with a Tar and a Zip file lies in 
> the methods tar_extraction_directory() and zip_extraction_directory() (in 
> [1]), which try to locate the deflated files:
> 
> * zip_extraction_directory() counts the number of non- .zip “files” in the 
> current directory. If more than one, the current path is returned ; if one, 
> this “file” is assumed to be the deflated directory, and the full path to 
> this directory is returned. The file_name variable (set to the name of the 
> downloaded file) is not used.
> 
> * tar_extraction_directory() which takes the name of the downloaded_file and 
> removes the extension. If a subdirectory of that name exists, it is returned. 
> Otherwise, if the full path to the downloaded file exists, the current path 
> is returned. Otherwise, an exception is raised.
> 
> This difference of behaviour can be very confusing. My wrapper local 
> installations kept failing because for my tool, the deflated directory name 
> did not match the tar.gz name. I was confused because I was using the bowtie 
> wrapper [2] as an example, where it is not an issue.
> 
> The obvious workaround is to use the target_filename attribute to have the 
> downloaded archive name match the subdirectory name (which I have done, and 
> it works perfectly now). But I was wondering if it would be a good idea to 
> harmonize both methods behaviour?
> 
> (P.S. As I am not very familiar yet with the Galaxy development process, I 
> believe posting here is appropriate ; but I’d be happy to open an issue − on 
> the Trello if I am not mistaken? − if needed.)
> 
> [1] 
> 
> [2] 
> 
> 
> Cheers,
> -- 
> Jean-Frédéric
> Bonsai Bioinformatics group
> ___
> 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/

___
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/

Re: [galaxy-dev] File Upload doesn't generate any activity

[Dannon Baker]

On Feb 4, 2013, at 10:36 AM, Hakeem Almabrazi  wrote:
> No there was nothing special about this installation.  I installed it on 
> CentOS and I tried to follow instructions in installing and configuring tools 
> and data.  The only thing that I did not was to test this feature before I 
> integrate it with postgres, nginx, tools such as bwa, samtools, bowtie etc.  
> I might have done something not right while doing so.  But once I was done 
> with all the configuration steps, I tried to load files via "Get Data" or 
> "Data Library".  It kept spinning and nothing is actually being written to 
> the system.  I tailed the logs and it was writing some logs every seconds but 
> no errors or warnings.  
> 
> The issue was resolved when I used "URL/Text" to go to this link as another 
> trail test.  After that everything works just fine.  Now we can load files 
> via either way.

Very strange, but I'm glad it's working for you now.  If this does crop up 
again, let me know and we can try to reproduce what's happening and fix it.

> The only error I keep seeing in the log is when we restart the server and 
> from what I read, this is a bug...
> 
> Traceback (most recent call last):
>  File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py",
> line 447, in _load_plugin
>module = __import__( module_name )
>  File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py",
> line 232
>worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), 
> target=self.run_next )
> ^
> SyntaxError: invalid syntax
> 
> 
> 
> Please let me know if you want me to do anything else that might help 
> debugging this issue.

This issue with the LWR has been fixed in changeset 8731:3299529e0fe8 which 
will be in the next distribution release.

-Dannon
___
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/

Re: [galaxy-dev] Toolshed tools minimal requirments for submission

[Bossers, Alex]

Greg and Björn, thanks for the info.

I will again review that section. Indeed a simple tool just required an xml, 
tool script and some README. But as you guessed I was more interested in 
complexer types; One might be the use of a bowtie2 multi mapper script we use 
to map fastq reads to a set of databases picked from the available bowtie 
indices within galaxy. Graphs are generated with R.

So of course the xml and wrapper scripts should be there as well as the R 
scripts.
How about bowtie2_db.lock additions?
How to secure R and bowtie2? Just by requirements?
And their licenses?

Thanks
Alex

Van: Greg Von Kuster [mailto:g...@bx.psu.edu]
Verzonden: maandag 4 februari 2013 16:25
Aan: Bossers, Alex
CC: galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] Toolshed tools minimal requirments for submission

Hello Alex,

In very general terms, a repository should include everything necessary for 
ensuring each if it's contained utilities is functionally correct when 
installed into a local Galaxy instance.  Categories of Galaxy utilities are 
Galaxy-specific tools, proprietary Galaxy datatypes, exported Galaxy workflows, 
3rd-party tool dependency definitions and repository dependency definitions.

I believe the content of the original tool shed wiki is mostly retained in the 
current wiki.  The original wiki was just divided into document sections, and a 
lot of new content has been added because of the many new tool shed features 
that have been introduced.  The main section detailing repository content it is 
here:  
http://wiki.galaxyproject.org/Tool%20Shed#The_contents_of_your_tool_shed_repository.
  This page include many related pages whose links are at the bottom of the 
page.

It is not possible to give a precise, but general definition of what should be 
included in all repositories because repositories can contain different types 
of Galaxy utilities.  Each of the sections of the wiki page link above 
describes how to include these various Galaxy utilities.

Even Galaxy tools fall into various categories.  For example, some are very 
simple, requiring no 3rd party tool dependencies and the tool form does not use 
dynamically generated select lists.  These generally only require a script and 
an XML file.  However, more complex Galaxy tools may require additional 
supporting content to be included in the repository (e.g., a 
tool_data_table_conf.xml.sample file. etc)

If you could provide more details about what types of utilities you are 
building, I can steer you to the wiki pages that provide information about 
those specific utilities.

Thanks!

Greg Von Kuster


On Feb 4, 2013, at 9:53 AM, Bossers, Alex wrote:


Hi All,

We are experimenting with local toolsheds for tool maintainability. On the old 
galaxy wiki I can remember there was a short tutorial or small description of 
the minimal requirements of a tool to be submitted to the toolshed. Actually we 
submitted some.
However we seem unable to retrieve the proper info from the updated wiki.
We did find info on single tools or suites, or more special cases, but a simple 
example/list of  how and what to include in a repository is missing (at least 
we cannot find itmight be an issue of wrong key words)..

Anyone has an idea where to find such a document?

Thanks
Alex



___
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/

___
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/

Re: [galaxy-dev] File Upload doesn't generate any activity

[Hakeem Almabrazi]

Thank you Dannon for looking into this.  

No there was nothing special about this installation.  I installed it on CentOS 
and I tried to follow instructions in installing and configuring tools and 
data.  The only thing that I did not was to test this feature before I 
integrate it with postgres, nginx, tools such as bwa, samtools, bowtie etc.  I 
might have done something not right while doing so.  But once I was done with 
all the configuration steps, I tried to load files via "Get Data" or "Data 
Library".  It kept spinning and nothing is actually being written to the 
system.  I tailed the logs and it was writing some logs every seconds but no 
errors or warnings.  

The issue was resolved when I used "URL/Text" to go to this link as another 
trail test.  After that everything works just fine.  Now we can load files via 
either way.

The only error I keep seeing in the log is when we restart the server and from 
what I read, this is a bug...

Traceback (most recent call last):
  File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py",
line 447, in _load_plugin
module = __import__( module_name )
  File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py",
line 232
worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), 
target=self.run_next )
 ^
SyntaxError: invalid syntax



Please let me know if you want me to do anything else that might help debugging 
this issue.

Regards,

-Original Message-
From: Dannon Baker [mailto:dannonba...@me.com] 
Sent: Sunday, February 03, 2013 7:14 PM
To: Hakeem Almabrazi
Cc: Stephen Groenewold; Galaxy Dev; galaxy-b...@bx.psu.edu Bugs
Subject: Re: [galaxy-dev] File Upload doesn't generate any activity

I just wanted to follow up on this and make sure everything was now working as 
expected.  I've tried to reproduce the original issue and have thus far been 
unsuccessful in doing so with a fresh instance.  Is the configuration of your 
Galaxy instance special in any way?  Did you notice any logged errors (either 
in the Javascript console or in Galaxy's log)?

-Dannon


On Feb 1, 2013, at 3:37 PM, Hakeem Almabrazi  wrote:

> Stephen,,,
>  
> Here is your solution:
>  
> In the Tools panel select "Get Data", "Upload File". You can either upload a 
> file, or enter one or more URLs in the "URL/Text" box. Enter 
> "http://galaxy.psu.edu/CPMB/TAF1_ChIP.txt"; in the box and click "Execute"
>  
> I am not sure what happened there but it seems this triggered some database 
> updates that was needed. 
>  
> It worked J
>  
>  
> From: galaxy-dev-boun...@lists.bx.psu.edu 
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Stephen Groenewold
> Sent: Friday, February 01, 2013 10:41 AM
> To: galaxy-dev@lists.bx.psu.edu
> Subject: [galaxy-dev] File Upload doesn't generate any activity
>  
> We've  installed a local instance of Galaxy and are having trouble with the 
> first step of uploading files. The only thing that will currently upload is 
> text pasted into the URL/Text box.
>  
> Any attempt to upload a file using the Browse File box not only fails, it 
> never even starts. It's as if the Execute button is disabled.
>  
> I've tried changing the ajax-upload parameter to "false" in 
> tools/data_source/upload.xml (as mentioned in a workaround posted to the list 
> by Daniel Blankenburg in Aug 2012). I've also tried using different browsers 
> (including Internet Explorer) and going the route of Adding Data Libraries as 
> Admin. None of those attempts have worked.
>  
> Am I missing a configuration setup? Could there be permissions issues on the 
> Galaxy machine?
>  
> Thanks.
>  
> Steve
>  
> ___
> 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/


___
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/

Re: [galaxy-dev] HTML output, hide "preview" text box?

[DePasse, Jay V]

Ah, I see, thanks Jeremy.

I did see the html entry in the datatypes_conf.xml, but (erroneously) thought 
that I was to use the datatype listed after the colon ("Html") rather than the 
extension (which is "html").



Setting my output type to "html" produces the desired behavior.

Thanks again,

-- Jay

On Feb 4, 2013, at 10:16 AM, Jeremy Goecks wrote:

My outputs section in the tool's xml file is:

  

  

You should set the output format to 'html' — all lower case. Galaxy has a list 
of known dataset types in datatypes.conf, and your output format should always 
match one of those in the file.

Finally, please always include the mailing list in your reply so that emails 
are tracked and archived.

Best,
J.


___
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/

Re: [galaxy-dev] Toolshed tools minimal requirments for submission

[Greg Von Kuster]

Hello Alex,

In very general terms, a repository should include everything necessary for 
ensuring each if it's contained utilities is functionally correct when 
installed into a local Galaxy instance.  Categories of Galaxy utilities are 
Galaxy-specific tools, proprietary Galaxy datatypes, exported Galaxy workflows, 
3rd-party tool dependency definitions and repository dependency definitions.

I believe the content of the original tool shed wiki is mostly retained in the 
current wiki.  The original wiki was just divided into document sections, and a 
lot of new content has been added because of the many new tool shed features 
that have been introduced.  The main section detailing repository content it is 
here:  
http://wiki.galaxyproject.org/Tool%20Shed#The_contents_of_your_tool_shed_repository.
  This page include many related pages whose links are at the bottom of the 
page.

It is not possible to give a precise, but general definition of what should be 
included in all repositories because repositories can contain different types 
of Galaxy utilities.  Each of the sections of the wiki page link above 
describes how to include these various Galaxy utilities.  

Even Galaxy tools fall into various categories.  For example, some are very 
simple, requiring no 3rd party tool dependencies and the tool form does not use 
dynamically generated select lists.  These generally only require a script and 
an XML file.  However, more complex Galaxy tools may require additional 
supporting content to be included in the repository (e.g., a 
tool_data_table_conf.xml.sample file. etc)

If you could provide more details about what types of utilities you are 
building, I can steer you to the wiki pages that provide information about 
those specific utilities.  

Thanks!

Greg Von Kuster


On Feb 4, 2013, at 9:53 AM, Bossers, Alex wrote:

> Hi All,
>  
> We are experimenting with local toolsheds for tool maintainability. On the 
> old galaxy wiki I can remember there was a short tutorial or small 
> description of the minimal requirements of a tool to be submitted to the 
> toolshed. Actually we submitted some.
> However we seem unable to retrieve the proper info from the updated wiki.
> We did find info on single tools or suites, or more special cases, but a 
> simple example/list of  how and what to include in a repository is missing 
> (at least we cannot find itmight be an issue of wrong key words)..
>  
> Anyone has an idea where to find such a document?
>  
> Thanks
> Alex
>  
>  
>  
> ___
> 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/

___
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/

Re: [galaxy-dev] HTML output, hide "preview" text box?

[Jeremy Goecks]

> My outputs section in the tool's xml file is:
> 
>   
> 
>   

You should set the output format to 'html' — all lower case. Galaxy has a list 
of known dataset types in datatypes.conf, and your output format should always 
match one of those in the file.

Finally, please always include the mailing list in your reply so that emails 
are tracked and archived.

Best,
J.

___
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/

Re: [galaxy-dev] Toolshed tools minimal requirments for submission

[Björn Grüning]

Hi Alex,

have a look at that page:

http://wiki.galaxyproject.org/Tool%
20Shed#The_contents_of_your_tool_shed_repository

In the near future a small sub community will review tools according to
these features. A rating system is already included in the current
toolshed.

Hope that helps a little bit.
Bjoern

> Hi All,
> We are experimenting with local toolsheds for tool maintainability. On
> the old galaxy wiki I can remember there was a short tutorial or small
> description of the minimal requirements of a tool to be submitted to
> the toolshed. Actually we submitted some.
> 
> However we seem unable to retrieve the proper info from the updated
> wiki.
> 
> We did find info on single tools or suites, or more special cases, but
> a simple example/list of  how and what to include in a repository is
> missing (at least we cannot find itmight be an issue of wrong key
> words)..
> 
>  
> 
> Anyone has an idea where to find such a document?
> 
>  
> 
> Thanks
> 
> Alex
> 
>  
> 
>  
> 
>  
> 
> 
> ___
> 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/

-- 
Björn Grüning
Albert-Ludwigs-Universität Freiburg
Institute of Pharmaceutical Sciences
Pharmaceutical Bioinformatics
Hermann-Herder-Strasse 9
D-79104 Freiburg i. Br.

Tel.:  +49 761 203-4872
Fax.:  +49 761 203-97769
E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
Web: http://www.pharmaceutical-bioinformatics.org/

___
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/

[galaxy-dev] Toolshed tools minimal requirments for submission

[Bossers, Alex]

Hi All,

We are experimenting with local toolsheds for tool maintainability. On the old 
galaxy wiki I can remember there was a short tutorial or small description of 
the minimal requirements of a tool to be submitted to the toolshed. Actually we 
submitted some.
However we seem unable to retrieve the proper info from the updated wiki.
We did find info on single tools or suites, or more special cases, but a simple 
example/list of  how and what to include in a repository is missing (at least 
we cannot find itmight be an issue of wrong key words)..

Anyone has an idea where to find such a document?

Thanks
Alex



___
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/