[galaxy-dev] GalaxyAdmins Meetup This Thursday

2016-06-14 Thread Dave Clements 
Hello all,

The June online meetup of GalaxyAdmins will be this Thursday
.
This month features two talks:


*1. Galaxy in Production at the University of Minnesota*

[image: Minnesota Supercomputing Institute] 



[image: Galaxy Radio Telescope]


Galaxy has been deployed in several contexts by the Minnesota
Supercomputing Institute (MSI)  at the University
of Minnesota - Twin Citites . This month Evan Bollig
 and JJ Johnson
 of MSI will discuss several aspects of
this work relevant to the GalaxyAdmins
 group:

   -

   customizations made to Galaxy that enable MSI to leverage it as a Tier I
   service  for our users (e.g.,
   scheduling, quotas, billing, and sharing).
   -

   Pulsar  for Galaxy-P
    tools on Windows.
   -

   the CLIA-certified
   

pipelines
   and how Galaxy is integrated into clinical workflows

*2. Galaxy Radio Telescope*

The GRT  aims to collect
job run information from Galaxy servers that opt into the process. Galaxy
Admins can sign in to the GRT, register their Galaxy servers, and get back
API keys per-Galaxy instance. Then they set up a cron job (preferably
weekly, but we may explore options here later), and submit job data to the
GRT.

See https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_06_16
for full details and links.  The conference room link will be posted an
hour before the meetup.

GalaxyAdmins is a discussion group for Galaxy community members that
administer Galaxy installations.

Hope to see you (online) on Thursday,

Dave Clements and Hans-Rudolf Hotz
-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/
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[galaxy-dev] Infinite recursion on conda dependency manager

2016-06-14 Thread Peter van Heusden 
Hi there

I've got a package in our lab conda channel (its still in testing phase)
called goget. This is specified as a requirement for the build_ctb_gene
tool like this:


   goget


When the tool runs, I see infinite recursion on the conda side:

https://gist.github.com/pvanheus/c16a07a2c954741a311881cc7606df8d

Any ideas?

Thanks,
Peter
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Re: [galaxy-dev] History is not up-to-date

2016-06-14 Thread Carl Eberhard 
Hi, Phillip

Quick questions:
- is the time properly set on the computer where you've got Galaxy running
in the browser?
- is the time in the docker container also correct?

>From you terminal output it looks like the update time might be the issue
and we can then take it from there. Thanks


On Tue, Jun 14, 2016 at 11:28 AM, Rathert, Philipp, Dr. <
philipp.rath...@ibc.uni-stuttgart.de> wrote:

> Dear All,
>
>
>
> I have a problem with my histories.
>
> We are running the Docker galaxy stable version 16.04 and when I start a
> tool the history does not show that it is running. it is not specific for
> any tool but for all.
>
>
>
>
>
>
>
> however, something is running in the back
>
>
> 129.69.102.30 - - [14/Jun/2016:12:57:21 +] "GET
> /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z
> HTTP/1.1" 200 - "http://129.69.102.42/"; "Mozilla/5.0 (Macintosh; Intel
> Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3
> Safari/601.4.4"
>
> [pid: 271|app: 0|req: 74/163] 129.69.102.30 () {44 vars in 964 bytes} [Tue
> Jun 14 12:57:21 2016] GET
> /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z
> => generated 2511 bytes in 33 msecs (HTTP/1.1 200) 3 headers in 124 bytes
> (1 switches on core 2)
>
> 129.69.102.30 - - [14/Jun/2016:12:57:25 +] "GET
> /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z
> HTTP/1.1" 200 - "http://129.69.102.42/"; "Mozilla/5.0 (Macintosh; Intel
> Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3
> Safari/601.4.4"
>
> [pid: 271|app: 0|req: 75/164] 129.69.102.30 () {44 vars in 964 bytes} [Tue
> Jun 14 12:57:25 2016] GET
> /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z
> => generated 2511 bytes in 29 msecs (HTTP/1.1 200) 3 headers in 124 bytes
> (1 switches on core 1)
>
> 129.69.102.30 - - [14/Jun/2016:12:57:29 +] "GET
> /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z
> HTTP/1.1" 200 - "http://129.69.102.42/"; "Mozilla/5.0 (Macintosh; Intel
> Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3
> Safari/601.4.4"
>
> [pid: 271|app: 0|req: 76/165] 129.69.102.30 () {44 vars in 964 bytes} [Tue
> Jun 14 12:57:29 2016] GET
> /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z
> => generated 2112 bytes in 30 msecs (HTTP/1.1 200) 3 headers in 124 bytes
> (1 switches on core 0)
>
> 129.69.102.30 - - [14/Jun/2016:12:57:33 +] "GET
> /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z
> HTTP/1.1" 200 - "http://129.69.102.42/"; "Mozilla/5.0 (Macintosh; Intel
> Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3
> Safari/601.4.4"
>
> [pid: 272|app: 0|req: 90/166] 129.69.102.30 () {44 vars in 964 bytes} [Tue
> Jun 14 12:57:33 2016] GET
> /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z
> => generated 2112 bytes in 32 msecs (HTTP/1.1 200) 3 headers in 124 bytes
> (1 switches on core 0)
>
> 129.69.102.30 - - [14/Jun/2016:12:57:37 +] "GET
> /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z
> HTTP/1.1" 200 - "http://129.69.102.42/"; "Mozilla/5.0 (Macintosh; Intel
> Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3
> Safari/601.4.4"
>
> [pid: 271|app: 0|req: 77/167] 129.69.102.30 () {44 vars in 964 bytes} [Tue
> Jun 14 12:57:37 2016] GET
> /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z
> => generated 2112 bytes in 27 msecs (HTTP/1.1 200) 3 headers in 124 bytes
> (1 switches on core 3)
>
>
>
>
>
> I am not sure how to fix this and I am happy for any suggestion.
>
>
> Cheers,
>
>
> Philipp
>
> ___
> 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:
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>
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Re: [galaxy-dev] how to get raw input from GUI

2016-06-14 Thread Dooley, Damion 
A general note, besides  which sounds like a fine choice, a
technique I've used where the form's input might have some wonky
characters in it, including carriage returns, but these need to be
received and processed via a command line, is to use encode():

$rules.encode('base64').replace('\n','')

Then over in receiving python script

Rules = rulesparam.decode('base64')

D.


>Message: 3
>Date: Mon, 13 Jun 2016 17:12:05 -0700
>From: Beginner TI 
>To: "galaxy-...@lists.bx.psu.edu" 
>Subject: [galaxy-dev] how to get raw input from GUI
>Message-ID:
>   
>Content-Type: text/plain; charset="utf-8"
>
>Hi,
>
>I am working on a wrapper for gatk and including
>
>help="--filterName, --filterExpression">
>title="Filter name to be included in the analysis" />
>title="Filter
>expression to be included in the analysis" />
>
>
>in it, however, when I reference it using
>
>${filter.filter_exp}
>
>it would translate 'FS > 30.0' into XXXFS __gt__ 30.0XXX
>
>is there a way that I could keep the original text string 'FS > 30.0'? I
>did a quick lookup online but didn't see anything in cheetah's user guide
>or other places.
>
>Thanks,
>Rui

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[galaxy-dev] History is not up-to-date

2016-06-14 Thread Rathert , Philipp , Dr . 
Dear All,





I have a problem with my histories. 

We are running the Docker galaxy stable version 16.04 and when I start a tool 
the history does not show that it is running. it is not specific for any tool 
but for all.














however, something is running in the back



129.69.102.30 - - [14/Jun/2016:12:57:21 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z
 HTTP/1.1" 200 - "http://129.69.102.42/  " "Mozilla/5.0 
(Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) 
Version/9.0.3 Safari/601.4.4"

[pid: 271|app: 0|req: 74/163] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:21 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z
 => generated 2511 bytes in 33 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 2)

129.69.102.30 - - [14/Jun/2016:12:57:25 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z
 HTTP/1.1" 200 - "http://129.69.102.42/  " "Mozilla/5.0 
(Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) 
Version/9.0.3 Safari/601.4.4"

[pid: 271|app: 0|req: 75/164] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:25 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z
 => generated 2511 bytes in 29 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 1)

129.69.102.30 - - [14/Jun/2016:12:57:29 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z
 HTTP/1.1" 200 - "http://129.69.102.42/  " "Mozilla/5.0 
(Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) 
Version/9.0.3 Safari/601.4.4"

[pid: 271|app: 0|req: 76/165] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:29 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z
 => generated 2112 bytes in 30 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 0)

129.69.102.30 - - [14/Jun/2016:12:57:33 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z
 HTTP/1.1" 200 - "http://129.69.102.42/  " "Mozilla/5.0 
(Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) 
Version/9.0.3 Safari/601.4.4"

[pid: 272|app: 0|req: 90/166] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:33 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z
 => generated 2112 bytes in 32 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 0)

129.69.102.30 - - [14/Jun/2016:12:57:37 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z
 HTTP/1.1" 200 - "http://129.69.102.42/  " "Mozilla/5.0 
(Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) 
Version/9.0.3 Safari/601.4.4"

[pid: 271|app: 0|req: 77/167] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:37 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z
 => generated 2112 bytes in 27 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 3)

 





I am not sure how to fix this and I am happy for any suggestion.



Cheers,



Philipp

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Re: [galaxy-dev] tabular file displayed without tabs

2016-06-14 Thread Dannon Baker 
Ok, so it's definitely the column limit that's causing the unexpected
style-less display.  This currently isn't configurable per-galaxy (the plan
was to add more appropriate displays for many-columned files), but here's a
quick gist to show you how you might tweak this locally:

https://gist.github.com/dannon/f67cccd16f9e8c8776a0032b11d1c5c7

This would be really easy to turn into an app configuration setting in
galaxy.ini if it seems like something folks would want though I opted not
to do so originally to avoid configuration bloat for what seemed like a
very niche case.

On Tue, Jun 14, 2016 at 10:23 AM Ryan G  wrote:

> No, it happens to all output from this particular tool.
>
> I do see a javascript warning in the console, 'The character encoding of a
> framed document was not declared.  The document may appear different if
> view without the document framing it.'
>
> The file does have 64 columns in it.  Is there a way to change Galaxy's
> default from 50 to something more?
>
>
>
> On Tue, May 31, 2016 at 8:17 AM, Carl Eberhard 
> wrote:
>
>> Strange. Alright, a few questions then:
>>
>> * Is this the only file that this happens to? Do other outputs from this
>> tool produce the same sort of error?
>> * Do you see any javascript errors in the console when attempting the
>> viewing? (how to here: http://webmasters.stackexchange.com/a/77337)
>>
>> On Fri, May 27, 2016 at 12:42 PM, Ryan G 
>> wrote:
>>
>>> The format is listed as tabular when I view details.
>>>
>>> In fact, in the preview window in the History Pane, it recognizes there
>>> are columns and that the data is in fact tabular, but when displaying, this
>>> isn't the case.
>>>
>>>
>>>
>>> On Tue, May 24, 2016 at 4:20 PM, Carl Eberhard 
>>> wrote:
>>>
 Ok - if it's not zebra striped and it's word wrapping, then it's
 somehow not displaying as tabular - you're correct.

 If you click on the 'View details' button of that dataset (the 'i' with
 the circle around it shown when the dataset is expanded in the right hand
 side of the 'Analyze Data' page), what does it list the 'Format' as?
 'tabular'? (This is also listed as 'Format' in the expanded view itself).

 On Mon, May 23, 2016 at 5:33 PM, Ryan G 
 wrote:

> Odd because I have another tabular file that is displayed with every
> other line highlighted and there is not word-wrapping on the file.  
> However
> the file that has the type tabular and displayed as text is word-wrapped
> with no lines highlighted.  I suspect its not actually recognized as
> tabular or is being overridden where.
>
>
> On Thu, Nov 12, 2015 at 10:23 AM, Carl Eberhard <
> carlfeberh...@gmail.com> wrote:
>
>> Hi, Ryan
>>
>> Galaxy displays tabular data in the browser using a  tag. It
>> *sounds like* the behavior you see (columns losing space between one
>> another when narrowing the window and getting more space as you expand 
>> the
>> window) would reflect that.
>>
>> Carl
>>
>> On Wed, Oct 28, 2015 at 1:23 PM, Ryan G 
>> wrote:
>>
>>> The file is an output from a tool and in the tool's xml, its format
>>> is tabular.
>>>
>>>
>>>
>>> On Tue, Oct 27, 2015 at 3:43 AM, Björn Grüning <
>>> bjoern.gruen...@gmail.com> wrote:
>>>
 Hi Ryan,

 is it recognised as 'tabular'?

 Ciao,
 Bjoern

 Am 27.10.2015 um 04:42 schrieb Ryan G:
 > Hi - I have a tools that generates a tab-delimited text file as
 output.
 > when I click the eye icon to view the data, all the fields are
 compressed
 > as if there were no tabs.  If I expand the history view, the
 little preview
 > window shows the contents as tabbed.  I've verified that the
 spaces are
 > indeed '\t' tab characters.  Why would Galaxy not display this
 file as a
 > tab-delimited file?
 >
 >
 >
 > ___
 > 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:
 >   https://lists.galaxyproject.org/
 >
 > To search Galaxy mailing lists use the unified search at:
 >   http://galaxyproject.org/search/mailinglists/
 >

>>>
>>>
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>   https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>   http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
>

>>

Re: [galaxy-dev] tabular file displayed without tabs

2016-06-14 Thread Ryan G 
No, it happens to all output from this particular tool.

I do see a javascript warning in the console, 'The character encoding of a
framed document was not declared.  The document may appear different if
view without the document framing it.'

The file does have 64 columns in it.  Is there a way to change Galaxy's
default from 50 to something more?



On Tue, May 31, 2016 at 8:17 AM, Carl Eberhard 
wrote:

> Strange. Alright, a few questions then:
>
> * Is this the only file that this happens to? Do other outputs from this
> tool produce the same sort of error?
> * Do you see any javascript errors in the console when attempting the
> viewing? (how to here: http://webmasters.stackexchange.com/a/77337)
>
> On Fri, May 27, 2016 at 12:42 PM, Ryan G 
> wrote:
>
>> The format is listed as tabular when I view details.
>>
>> In fact, in the preview window in the History Pane, it recognizes there
>> are columns and that the data is in fact tabular, but when displaying, this
>> isn't the case.
>>
>>
>>
>> On Tue, May 24, 2016 at 4:20 PM, Carl Eberhard 
>> wrote:
>>
>>> Ok - if it's not zebra striped and it's word wrapping, then it's somehow
>>> not displaying as tabular - you're correct.
>>>
>>> If you click on the 'View details' button of that dataset (the 'i' with
>>> the circle around it shown when the dataset is expanded in the right hand
>>> side of the 'Analyze Data' page), what does it list the 'Format' as?
>>> 'tabular'? (This is also listed as 'Format' in the expanded view itself).
>>>
>>> On Mon, May 23, 2016 at 5:33 PM, Ryan G 
>>> wrote:
>>>
 Odd because I have another tabular file that is displayed with every
 other line highlighted and there is not word-wrapping on the file.  However
 the file that has the type tabular and displayed as text is word-wrapped
 with no lines highlighted.  I suspect its not actually recognized as
 tabular or is being overridden where.


 On Thu, Nov 12, 2015 at 10:23 AM, Carl Eberhard <
 carlfeberh...@gmail.com> wrote:

> Hi, Ryan
>
> Galaxy displays tabular data in the browser using a  tag. It
> *sounds like* the behavior you see (columns losing space between one
> another when narrowing the window and getting more space as you expand the
> window) would reflect that.
>
> Carl
>
> On Wed, Oct 28, 2015 at 1:23 PM, Ryan G 
> wrote:
>
>> The file is an output from a tool and in the tool's xml, its format
>> is tabular.
>>
>>
>>
>> On Tue, Oct 27, 2015 at 3:43 AM, Björn Grüning <
>> bjoern.gruen...@gmail.com> wrote:
>>
>>> Hi Ryan,
>>>
>>> is it recognised as 'tabular'?
>>>
>>> Ciao,
>>> Bjoern
>>>
>>> Am 27.10.2015 um 04:42 schrieb Ryan G:
>>> > Hi - I have a tools that generates a tab-delimited text file as
>>> output.
>>> > when I click the eye icon to view the data, all the fields are
>>> compressed
>>> > as if there were no tabs.  If I expand the history view, the
>>> little preview
>>> > window shows the contents as tabbed.  I've verified that the
>>> spaces are
>>> > indeed '\t' tab characters.  Why would Galaxy not display this
>>> file as a
>>> > tab-delimited file?
>>> >
>>> >
>>> >
>>> > ___
>>> > 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:
>>> >   https://lists.galaxyproject.org/
>>> >
>>> > To search Galaxy mailing lists use the unified search at:
>>> >   http://galaxyproject.org/search/mailinglists/
>>> >
>>>
>>
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
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>>   http://galaxyproject.org/search/mailinglists/
>>
>
>

>>>
>>
>
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Re: [galaxy-dev] cleanup datasets error

2016-06-14 Thread Bjoern Gruening 

Wuhu!

On 14.06.2016 11:25, Philipp Rathert wrote:

RE: [galaxy-dev] cleanup datasets error

Hi Bjoern,

Works now.

Thank you very much,

Philipp

*From:*Bjoern Gruening [mailto:bjoern.gruen...@gmail.com]
*Sent:* Tuesday, June 14, 2016 11:07 AM
*To:* Rathert, Philipp, Dr. 
*Cc:* galaxy-dev 
*Subject:* Re: [galaxy-dev] cleanup datasets error

Hi,

can you please do this before executing the script. This will source 
your Galaxy virtual-env.


"""
source $GALAXY_VIRTUAL_ENV/bin/activate
"""

Ciao,
Bjoern


On 14.06.2016 11:01, Rathert, Philipp, Dr. wrote:

Hi Bjoern,



I edited the galaxy.ini directly and started the script.
Unfortunately I get a different error:





Traceback (most recent call last):

File "scripts/cleanup_datasets/cleanup_datasets.py", line 544, in


  main()

File "scripts/cleanup_datasets/cleanup_datasets.py", line 104, in main

  app = CleanupDatasetsApplication( config )

File "scripts/cleanup_datasets/cleanup_datasets.py", line 529, in
__init__

  self.model = galaxy.model.mapping.init( config.file_path,
config.database_connection, engine_options={},
create_tables=False, object_store=self.object_store )

File "/galaxy-central/lib/galaxy/model/mapping.py", line 2541, in init

  engine = build_engine( url, engine_options,
database_query_profiling_proxy, trace_logger )

File "/galaxy-central/lib/galaxy/model/orm/engine_factory.py",
line 20, in build_engine

  engine = create_engine( url, proxy=proxy, **engine_options )

File

"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/__init__.py",
line 386, in create_engine

  return strategy.create(*args, **kwargs)

File

"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py",
line 75, in create

  dbapi = dialect_cls.dbapi(**dbapi_args)

File

"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py",
line 579, in dbapi

  import psycopg2

ImportError: No module named psycopg2



Can I install the python-psycopq2 module via apt-get in the
container and would this help to fix thee issue?



Cheers,



Philipp



-Original message-
*From:* Rathert, Philipp, Dr.


*Sent:* Tuesday 14th June 2016 9:56
*To:* Bjoern Gruening 

*Cc:* galaxy-dev 

*Subject:* Re: [galaxy-dev] cleanup datasets error


Hi Bjoern,

This is wired. It worked before...

I will add this to the galaxy.ini in the config folder and try
again.

Cheers,

Philipp

---Philipp on the road---


Am 14.06.2016 um 09:50 schrieb Bjoern Gruening
mailto:bjoern.gruen...@gmail.com>>:

Hi,

I don't think this will work with the script. This script
reads the config file you specify config/galaxy.ini. And
hence it needs to be added in this file, not via -e variables.
This is probably something we should improve.

Ciao,
Bjoern


> cleanup datasets

error

>

> HI Björn,

>

>

>

> I have added these to the galaxy.ini via
the docker

specific e-

> variables during startup of the container.

>

>

>

> How can I check if they are broken?

>

>

>

> Cheers,

>

>

>

> Philipp

>

>

>

> *From:*Bjoern Gruening
[mailto:bjoern.gruen...@gmail.com]

*Sent:*

> Tuesday, June 14, 2016 9:30 AM *To:*
Rathert,

Philipp, Dr.

> 
;

galaxy-dev

> 


*Subject:* Re: [galaxy-dev]

> cleanup datasets error

>

>

>

> Hi Philipp,

Re: [galaxy-dev] cleanup datasets error

2016-06-14 Thread Philipp Rathert 
Hi Bjoern,

 

Works now. 

Thank you very much,

 

Philipp

 

From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] 
Sent: Tuesday, June 14, 2016 11:07 AM
To: Rathert, Philipp, Dr. 
Cc: galaxy-dev 
Subject: Re: [galaxy-dev] cleanup datasets error

 

Hi,

can you please do this before executing the script. This will source your 
Galaxy virtual-env.

"""
source $GALAXY_VIRTUAL_ENV/bin/activate
"""

Ciao,
Bjoern




On 14.06.2016 11:01, Rathert, Philipp, Dr. wrote:

Hi Bjoern,







I edited the galaxy.ini directly and started the script. Unfortunately I get a 
different error:









Traceback (most recent call last):

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 544, in 

main()

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 104, in main

app = CleanupDatasetsApplication( config )

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 529, in __init__

self.model = galaxy.model.mapping.init( config.file_path, 
config.database_connection, engine_options={}, create_tables=False, 
object_store=self.object_store )

  File "/galaxy-central/lib/galaxy/model/mapping.py", line 2541, in init

engine = build_engine( url, engine_options, database_query_profiling_proxy, 
trace_logger )

  File "/galaxy-central/lib/galaxy/model/orm/engine_factory.py", line 20, in 
build_engine

engine = create_engine( url, proxy=proxy, **engine_options )

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/__init__.py",
 line 386, in create_engine

return strategy.create(*args, **kwargs)

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py",
 line 75, in create

dbapi = dialect_cls.dbapi(**dbapi_args)

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py",
 line 579, in dbapi

import psycopg2

ImportError: No module named psycopg2





Can I install the python-psycopq2 module via apt-get in the container and would 
this help to fix thee issue?





Cheers,





Philipp





-Original message-
From: Rathert, Philipp, Dr.   

Sent: Tuesday 14th June 2016 9:56
To: Bjoern Gruening   

Cc: galaxy-dev   

Subject: Re: [galaxy-dev] cleanup datasets error




Hi Bjoern,

 

This is wired. It worked before...

I will add this to the galaxy.ini in the config folder and try again.

 

Cheers,

Philipp

---Philipp on the road---


Am 14.06.2016 um 09:50 schrieb Bjoern Gruening mailto:bjoern.gruen...@gmail.com> >:

Hi,

I don't think this will work with the script. This script reads the config file 
you specify config/galaxy.ini. And hence it needs to be added in this file, not 
via -e variables.
This is probably something we should improve.

Ciao,
Bjoern


> cleanup datasets

error



> 



> HI Björn,



> 



> 



> 



> I have added these to the galaxy.ini via the docker

specific e-



> variables during startup of the container.



> 



> 



> 



> How can I check if they are broken?



> 



> 



> 



> Cheers,



> 



> 



> 



> Philipp



> 



> 



> 



> *From:*Bjoern Gruening [mailto:bjoern.gruen...@gmail.com]

*Sent:*



> Tuesday, June 14, 2016 9:30 AM *To:* Rathert,

Philipp, Dr.



>   
;

galaxy-dev



>   


*Subject:* Re: [galaxy-dev]



> cleanup datasets error



> 



> 



> 



> Hi Philipp,



> 



> have you followed this from the readme?



> 



> 



> Note that if you would like to run any of the

cleanup scripts



>

 

 
,



> you will need to add the following to



> |/export/galaxy-central/config/galaxy.ini|:



> 



> |database_connection =



> postgresql://galaxy:galaxy@localhost:5432/galaxy|

|file_path =



> /export/galaxy-central/database/files|



>

Re: [galaxy-dev] cleanup datasets error

2016-06-14 Thread Bjoern Gruening 

Hi,

can you please do this before executing the script. This will source 
your Galaxy virtual-env.


"""
source $GALAXY_VIRTUAL_ENV/bin/activate
"""

Ciao,
Bjoern



On 14.06.2016 11:01, Rathert, Philipp, Dr. wrote:

RE: [galaxy-dev] cleanup datasets error

Hi Bjoern,


I edited the galaxy.ini directly and started the script. Unfortunately 
I get a different error:




Traceback (most recent call last):

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 544, in 



main()

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 104, in main

app = CleanupDatasetsApplication( config )

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 529, in 
__init__


self.model = galaxy.model.mapping.init( config.file_path, 
config.database_connection, engine_options={}, create_tables=False, 
object_store=self.object_store )


  File "/galaxy-central/lib/galaxy/model/mapping.py", line 2541, in init

engine = build_engine( url, engine_options, 
database_query_profiling_proxy, trace_logger )


  File "/galaxy-central/lib/galaxy/model/orm/engine_factory.py", line 
20, in build_engine


engine = create_engine( url, proxy=proxy, **engine_options )

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/__init__.py", 
line 386, in create_engine


return strategy.create(*args, **kwargs)

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", 
line 75, in create


dbapi = dialect_cls.dbapi(**dbapi_args)

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py", 
line 579, in dbapi


import psycopg2

ImportError: No module named psycopg2


Can I install the python-psycopq2 module via apt-get in the container 
and would this help to fix thee issue?



Cheers,


Philipp


-Original message-
*From:* Rathert, Philipp, Dr. 
*Sent:* Tuesday 14th June 2016 9:56
*To:* Bjoern Gruening 
*Cc:* galaxy-dev 
*Subject:* Re: [galaxy-dev] cleanup datasets error

Hi Bjoern,

This is wired. It worked before...
I will add this to the galaxy.ini in the config folder and try again.

Cheers,
Philipp

---Philipp on the road---

Am 14.06.2016 um 09:50 schrieb Bjoern Gruening
mailto:bjoern.gruen...@gmail.com>>:


Hi,

I don't think this will work with the script. This script reads
the config file you specify config/galaxy.ini. And hence it needs
to be added in this file, not via -e variables.
This is probably something we should improve.

Ciao,
Bjoern


> cleanup datasets error
>
> HI Björn,
>
>
>
> I have added these to the galaxy.ini via the docker specific e-
> variables during startup of the container.
>
>
>
> How can I check if they are broken?
>
>
>
> Cheers,
>
>
>
> Philipp
>
>
>
> *From:*Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] *Sent:*
> Tuesday, June 14, 2016 9:30 AM *To:* Rathert, Philipp, Dr.
> ; galaxy-dev
>  *Subject:* Re: [galaxy-dev]
> cleanup datasets error
>
>
>
> Hi Philipp,
>
> have you followed this from the readme?
>
>
> Note that if you would like to run any of the cleanup scripts
>

,
> you will need to add the following to
> |/export/galaxy-central/config/galaxy.ini|:
>
> |database_connection =
> postgresql://galaxy:galaxy@localhost:5432/galaxy| |file_path =
> /export/galaxy-central/database/files|
>
> Or is this broken? Cheers, Bjoern
>
> On 14.06.2016 09:21, Rathert, Philipp, Dr. wrote:
>
> Dear all,
>
>
>
> when I want to start the cleanup datasets script I get the
following
> error.
>
>
>
> (.venv)root@galaxy:/galaxy-central# python
> /galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py
> config/galaxy.ini -d -10 -1
>
> Traceback (most recent call last):
>
> File
"/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
> line 544, in 
>
> main()
>
> File
"/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
> line 99, in main
>
> for key, value in config_parser.items( "app:main" ):
>
> File "/usr/lib/python2.7/ConfigParser.py", line 642, in items
>
> raise NoSectionError(section)
>
> ConfigParser.NoSectionError: No section: 'app:main'
>
>
>
>
>
> We are using the docker galaxy stable 16.04 version. Before this
> script always worked without producing any error.
>
>
>
> It would be great if anybody has an idea how to fix this...
>
>
>
> Thank you very much in advance.
>
>
>
> Cheers,
>
>
>
> Philipp
>
>
>

Re: [galaxy-dev] cleanup datasets error

2016-06-14 Thread Rathert , Philipp , Dr . 
Hi Bjoern,



I edited the galaxy.ini directly and started the script. Unfortunately I get a 
different error:





Traceback (most recent call last):

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 544, in 

    main()

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 104, in main

    app = CleanupDatasetsApplication( config )

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 529, in __init__

    self.model = galaxy.model.mapping.init( config.file_path, 
config.database_connection, engine_options={}, create_tables=False, 
object_store=self.object_store )

  File "/galaxy-central/lib/galaxy/model/mapping.py", line 2541, in init

    engine = build_engine( url, engine_options, database_query_profiling_proxy, 
trace_logger )

  File "/galaxy-central/lib/galaxy/model/orm/engine_factory.py", line 20, in 
build_engine

    engine = create_engine( url, proxy=proxy, **engine_options )

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/__init__.py",
 line 386, in create_engine

    return strategy.create(*args, **kwargs)

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py",
 line 75, in create

    dbapi = dialect_cls.dbapi(**dbapi_args)

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py",
 line 579, in dbapi

    import psycopg2

ImportError: No module named psycopg2



Can I install the python-psycopq2 module via apt-get in the container and would 
this help to fix thee issue?



Cheers,



Philipp



-Original message-
From: Rathert, Philipp, Dr. 
Sent: Tuesday 14th June 2016 9:56
To: Bjoern Gruening 
Cc: galaxy-dev 
Subject: Re: [galaxy-dev] cleanup datasets error

Hi Bjoern,

This is wired. It worked before...
I will add this to the galaxy.ini in the config folder and try again.

Cheers,
Philipp

---Philipp on the road---

Am 14.06.2016 um 09:50 schrieb Bjoern Gruening mailto:bjoern.gruen...@gmail.com> >:

 Hi,
 
 I don't think this will work with the script. This script reads the config 
file you specify config/galaxy.ini. And hence it needs to be added in this 
file, not via -e variables.
 This is probably something we should improve.
 
 Ciao,
 Bjoern
 
 
 > cleanup datasets error
 > 
 > HI Björn,
 > 
 > 
 > 
 > I have added these to the galaxy.ini via the docker specific e-
 > variables during startup of the container.
 > 
 > 
 > 
 > How can I check if they are broken?
 > 
 > 
 > 
 > Cheers,
 > 
 > 
 > 
 > Philipp
 > 
 > 
 > 
 > *From:*Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] *Sent:*
 > Tuesday, June 14, 2016 9:30 AM *To:* Rathert, Philipp, Dr.
 > ; galaxy-dev
 >  *Subject:* Re: [galaxy-dev]
 > cleanup datasets error
 > 
 > 
 > 
 > Hi Philipp,
 > 
 > have you followed this from the readme?
 > 
 > 
 > Note that if you would like to run any of the cleanup scripts
 >,
 > you will need to add the following to
 > |/export/galaxy-central/config/galaxy.ini|:
 > 
 > |database_connection =
 > postgresql://galaxy:galaxy@localhost:5432/galaxy| |file_path =
 > /export/galaxy-central/database/files|
 > 
 > Or is this broken? Cheers, Bjoern
 > 
 > On 14.06.2016 09:21, Rathert, Philipp, Dr. wrote:
 > 
 > Dear all,
 > 
 > 
 > 
 > when I want to start the cleanup datasets script I get the following
 > error.
 > 
 > 
 > 
 > (.venv)root@galaxy:/galaxy-central# python
 > /galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py
 > config/galaxy.ini -d -10 -1
 > 
 > Traceback (most recent call last):
 > 
 > File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
 > line 544, in 
 > 
 > main()
 > 
 > File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
 > line 99, in main
 > 
 > for key, value in config_parser.items( "app:main" ):
 > 
 > File "/usr/lib/python2.7/ConfigParser.py", line 642, in items
 > 
 > raise NoSectionError(section)
 > 
 > ConfigParser.NoSectionError: No section: 'app:main'
 > 
 > 
 > 
 > 
 > 
 > We are using the docker galaxy stable 16.04 version. Before this
 > script always worked without producing any error.
 > 
 > 
 > 
 > It would be great if anybody has an idea how to fix this...
 > 
 > 
 > 
 > Thank you very much in advance.
 > 
 > 
 > 
 > Cheers,
 > 
 > 
 > 
 > Philipp
 > 
 > 
 > 
 > 
 > 
 > -Original message- *From:* Marius van den Beek
 >   *Sent:*
 > Tuesday 7th June 2016 14:06 *To:* Marco Tangaro
 >   *Cc:* galaxy-dev
 > 
 >  *Subject:* Re:
 > [galaxy-dev] Python tool wrapper with multiple input and output
 > files
 > 
 > 
 > Hi Marco,
 > 
 > 
 > 
 > you've got an interesting use-case there.
 > 
 > You may want to use either a dataset list (if you only supply
 > rna_n.bam),
 > 
 > or a paired dataset list (rna_n.bam and dna_n.bam).
 > 
 > I would probably implement a conditi

Re: [galaxy-dev] cleanup datasets error

2016-06-14 Thread Rathert , Philipp , Dr . 
Hi Bjoern,

This is wired. It worked before...
I will add this to the galaxy.ini in the config folder and try again.

Cheers,
Philipp

---Philipp on the road---

Am 14.06.2016 um 09:50 schrieb Bjoern Gruening mailto:bjoern.gruen...@gmail.com> >:

 Hi,
 
 I don't think this will work with the script. This script reads the config 
file you specify config/galaxy.ini. And hence it needs to be added in this 
file, not via -e variables.
 This is probably something we should improve.
 
 Ciao,
 Bjoern
 
 
 > cleanup datasets error
 > 
 > HI Björn,
 > 
 > 
 > 
 > I have added these to the galaxy.ini via the docker specific e-
 > variables during startup of the container.
 > 
 > 
 > 
 > How can I check if they are broken?
 > 
 > 
 > 
 > Cheers,
 > 
 > 
 > 
 > Philipp
 > 
 > 
 > 
 > *From:*Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] *Sent:*
 > Tuesday, June 14, 2016 9:30 AM *To:* Rathert, Philipp, Dr.
 > ; galaxy-dev
 >  *Subject:* Re: [galaxy-dev]
 > cleanup datasets error
 > 
 > 
 > 
 > Hi Philipp,
 > 
 > have you followed this from the readme?
 > 
 > 
 > Note that if you would like to run any of the cleanup scripts
 >,
 > you will need to add the following to
 > |/export/galaxy-central/config/galaxy.ini|:
 > 
 > |database_connection =
 > postgresql://galaxy:galaxy@localhost:5432/galaxy| |file_path =
 > /export/galaxy-central/database/files|
 > 
 > Or is this broken? Cheers, Bjoern
 > 
 > On 14.06.2016 09:21, Rathert, Philipp, Dr. wrote:
 > 
 > Dear all,
 > 
 > 
 > 
 > when I want to start the cleanup datasets script I get the following
 > error.
 > 
 > 
 > 
 > (.venv)root@galaxy:/galaxy-central# python
 > /galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py
 > config/galaxy.ini -d -10 -1
 > 
 > Traceback (most recent call last):
 > 
 > File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
 > line 544, in 
 > 
 > main()
 > 
 > File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
 > line 99, in main
 > 
 > for key, value in config_parser.items( "app:main" ):
 > 
 > File "/usr/lib/python2.7/ConfigParser.py", line 642, in items
 > 
 > raise NoSectionError(section)
 > 
 > ConfigParser.NoSectionError: No section: 'app:main'
 > 
 > 
 > 
 > 
 > 
 > We are using the docker galaxy stable 16.04 version. Before this
 > script always worked without producing any error.
 > 
 > 
 > 
 > It would be great if anybody has an idea how to fix this...
 > 
 > 
 > 
 > Thank you very much in advance.
 > 
 > 
 > 
 > Cheers,
 > 
 > 
 > 
 > Philipp
 > 
 > 
 > 
 > 
 > 
 > -Original message- *From:* Marius van den Beek
 >   *Sent:*
 > Tuesday 7th June 2016 14:06 *To:* Marco Tangaro
 >   *Cc:* galaxy-dev
 > 
 >  *Subject:* Re:
 > [galaxy-dev] Python tool wrapper with multiple input and output
 > files
 > 
 > 
 > Hi Marco,
 > 
 > 
 > 
 > you've got an interesting use-case there.
 > 
 > You may want to use either a dataset list (if you only supply
 > rna_n.bam),
 > 
 > or a paired dataset list (rna_n.bam and dna_n.bam).
 > 
 > I would probably implement a conditional, where the user selects
 > either a dataset list or a paired dataset list.
 > 
 > The output would then be another collection of output files.
 > 
 > Have a look at the test tool folder, and see if any of the tools
 > named collection_*.xml fits what you would like to do
 > 
 > https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools
 >
 >
 > 
 These two may be a good basis for what you want to achieve:
 > 
 >https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_creates_list.xml
 >
 >
 > 
 [this one creates an output collection]
 > 
 >https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_two_paired.xml
 >
 >
 > 
 [this one has a conditional to either select a list or a paired list as input]
 > 
 > 
 > 
 > Let us know if you need more help!
 > 
 > 
 > 
 > Cheers,
 > 
 > Marius
 > 
 > 
 > 
 > On 7 June 2016 at 09:50, Marco Tangaro  > wrote:
 > 
 > Dear experts, my name is Marco and I'm working to port our python
 > tool to the Galaxy framework. The main script needs a rna.bam file as
 > input, a reference fasta file, both mandatory. Finally, you can add a
 > dna.bam file, but this is optional. Therefore an example command is:
 > 
 > script.py -i rna.bam -f reference.fa -j dna.bam
 > 
 > The outout is a tabular. Again the -j dna.bam option is completely
 > optional. So quite soon it turned out that I had to use a python
 > wrapper to parse our script. Now the wrapper works fine.
 > 
 > 
 > The next step is to run the tool over multiple input file and we
 > would like to avoid to use a workflow.
 > 
 > The idea is that to each input file corresponds an output file. The
 > reference is still the same. For instance, we have:
 > 
 > rna_1.bam + d

Re: [galaxy-dev] cleanup datasets error

2016-06-14 Thread Bjoern Gruening 

Hi,

I don't think this will work with the script. This script reads the 
config file you specify config/galaxy.ini. And hence it needs to be 
added in this file, not via -e variables.

This is probably something we should improve.

Ciao,
Bjoern



cleanup datasets error

>
> HI Björn,
>
>
>
> I have added these to the galaxy.ini via the docker specific e-
> variables during startup of the container.
>
>
>
> How can I check if they are broken?
>
>
>
> Cheers,
>
>
>
> Philipp
>
>
>
> *From:*Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] *Sent:*
> Tuesday, June 14, 2016 9:30 AM *To:* Rathert, Philipp, Dr.
> ; galaxy-dev
>  *Subject:* Re: [galaxy-dev]
> cleanup datasets error
>
>
>
> Hi Philipp,
>
> have you followed this from the readme?
>
>
> Note that if you would like to run any of the cleanup scripts
> 
,

> you will need to add the following to
> |/export/galaxy-central/config/galaxy.ini|:
>
> |database_connection =
> postgresql://galaxy:galaxy@localhost:5432/galaxy| |file_path =
> /export/galaxy-central/database/files|
>
> Or is this broken? Cheers, Bjoern
>
> On 14.06.2016 09:21, Rathert, Philipp, Dr. wrote:
>
> Dear all,
>
>
>
> when I want to start the cleanup datasets script I get the following
> error.
>
>
>
> (.venv)root@galaxy:/galaxy-central# python
> /galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py
> config/galaxy.ini -d -10 -1
>
> Traceback (most recent call last):
>
> File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
> line 544, in 
>
> main()
>
> File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
> line 99, in main
>
> for key, value in config_parser.items( "app:main" ):
>
> File "/usr/lib/python2.7/ConfigParser.py", line 642, in items
>
> raise NoSectionError(section)
>
> ConfigParser.NoSectionError: No section: 'app:main'
>
>
>
>
>
> We are using the docker galaxy stable 16.04 version. Before this
> script always worked without producing any error.
>
>
>
> It would be great if anybody has an idea how to fix this...
>
>
>
> Thank you very much in advance.
>
>
>
> Cheers,
>
>
>
> Philipp
>
>
>
>
>
> -Original message- *From:* Marius van den Beek
>   *Sent:*
> Tuesday 7th June 2016 14:06 *To:* Marco Tangaro
>   *Cc:* galaxy-dev
> 
>  *Subject:* Re:
> [galaxy-dev] Python tool wrapper with multiple input and output
> files
>
>
> Hi Marco,
>
>
>
> you've got an interesting use-case there.
>
> You may want to use either a dataset list (if you only supply
> rna_n.bam),
>
> or a paired dataset list (rna_n.bam and dna_n.bam).
>
> I would probably implement a conditional, where the user selects
> either a dataset list or a paired dataset list.
>
> The output would then be another collection of output files.
>
> Have a look at the test tool folder, and see if any of the tools
> named collection_*.xml fits what you would like to do
>
> https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools
>
>
>
These two may be a good basis for what you want to achieve:


> 
https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_creates_list.xml

>
>
>
[this one creates an output collection]


> 
https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_two_paired.xml

>
>
>
[this one has a conditional to either select a list or a paired list as 
input]



>
>
> Let us know if you need more help!
>
>
>
> Cheers,
>
> Marius
>
>
>
> On 7 June 2016 at 09:50, Marco Tangaro  > wrote:
>
> Dear experts, my name is Marco and I'm working to port our python
> tool to the Galaxy framework. The main script needs a rna.bam file as
> input, a reference fasta file, both mandatory. Finally, you can add a
> dna.bam file, but this is optional. Therefore an example command is:
>
> script.py -i rna.bam -f reference.fa -j dna.bam
>
> The outout is a tabular. Again the -j dna.bam option is completely
> optional. So quite soon it turned out that I had to use a python
> wrapper to parse our script. Now the wrapper works fine.
>
>
> The next step is to run the tool over multiple input file and we
> would like to avoid to use a workflow.
>
> The idea is that to each input file corresponds an output file. The
> reference is still the same. For instance, we have:
>
> rna_1.bam + dna_1.bam -> output_1.txt rna_2.bam + dna_2.bam ->
> output_2.txt rna_3.bam + dna_3.bam -> output_3.txt ... and so on.
>
>
> But I don't know the best strategy to give to my wrapper multiple
> input files. Moreover I have to be sure, when the dna_xyz.bam files
> are uploaded, that they correspond to the right rna_xyz.bam file.
>
> I would like to have as output a page which is showing as results the
> link to the single output files as suggested here.
> https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files

Re: [galaxy-dev] cleanup datasets error

2016-06-14 Thread Philipp Rathert 
HI Björn,

 

I have added these to the galaxy.ini via the docker specific e- variables 
during startup of the container.

 

How can I check if they are broken?

 

Cheers,

 

Philipp

 

From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] 
Sent: Tuesday, June 14, 2016 9:30 AM
To: Rathert, Philipp, Dr. ; galaxy-dev 

Subject: Re: [galaxy-dev] cleanup datasets error

 

Hi Philipp,

have you followed this from the readme?




Note that if you would like to run any of the  

 cleanup scripts, you will need to add the following to 
/export/galaxy-central/config/galaxy.ini:

database_connection = postgresql://galaxy:galaxy@localhost:5432/galaxy
file_path = /export/galaxy-central/database/files

Or is this broken?
Cheers,
Bjoern



On 14.06.2016 09:21, Rathert, Philipp, Dr. wrote:

Dear all,







when I want to start the cleanup datasets script I get the following error.





(.venv)root@galaxy:/galaxy-central# python 
/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini 
-d -10 -1

Traceback (most recent call last):

  File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", line 
544, in 

main()

  File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", line 99, 
in main

for key, value in config_parser.items( "app:main" ):

  File "/usr/lib/python2.7/ConfigParser.py", line 642, in items

raise NoSectionError(section)

ConfigParser.NoSectionError: No section: 'app:main'









We are using the docker galaxy stable 16.04 version. Before this script always 
worked without producing any error. 







It would be great if anybody has an idea how to fix this...





Thank you very much in advance.





Cheers,





Philipp 









-Original message-
From: Marius van den Beek   

Sent: Tuesday 7th June 2016 14:06
To: Marco Tangaro   
Cc: galaxy-dev   

Subject: Re: [galaxy-dev] Python tool wrapper with multiple input and output 
files




Hi Marco, 

 

you've got an interesting use-case there.

You may want to use either a dataset list (if you only supply rna_n.bam),

or a paired dataset list (rna_n.bam and dna_n.bam). 

I would probably implement a conditional, where the user selects either a 
dataset list or a paired dataset list.

The output would then be another collection of output files.

Have a look at the test tool folder, and see if any of the tools named 
collection_*.xml fits what you would like to do

https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools

These two may be a good basis for what you want to achieve:

https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_creates_list.xml

[this one creates an output collection]

https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_two_paired.xml

[this one has a conditional to either select a list or a paired list as input]

 

Let us know if you need more help!

 

Cheers,

Marius

 

On 7 June 2016 at 09:50, Marco Tangaro mailto:ma.tang...@gmail.com> > wrote:

Dear experts,
my name is Marco and I'm working to port our python tool to the Galaxy 
framework.
The main script needs a rna.bam file as input, a reference fasta file, both 
mandatory. Finally, you can add a dna.bam file, but this is optional.
Therefore an example command is:

script.py -i rna.bam -f reference.fa -j dna.bam

The outout is a tabular.
Again the -j dna.bam option is completely optional.
So quite soon it turned out that I had to use a python wrapper to parse our 
script. Now the wrapper works fine.


The next step is to run the tool over multiple input file and we would like to 
avoid to use a workflow.

The idea is that to each input file corresponds an output file. The reference 
is still the same.
For instance, we have:

rna_1.bam + dna_1.bam -> output_1.txt
rna_2.bam + dna_2.bam -> output_2.txt
rna_3.bam + dna_3.bam -> output_3.txt
...
and so on.


But I don't know the best strategy to give to my wrapper multiple input files.
Moreover I have to be sure, when the dna_xyz.bam files are uploaded, that they 
correspond to the right rna_xyz.bam file.

I would like to have as output a page which is showing as results the link to 
the single output files as suggested here.
https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
planning to integrate a javascript interface.

I've browsed a lot, but on multiple input file the posts are old.
I'm using the last galaxy release (16_04).

I'm quite new to the galaxy world...
Thanks a lot for your suggestions,
Marco


___
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:
  https://lists.galaxyproject.org/

To

Re: [galaxy-dev] cleanup datasets error

2016-06-14 Thread Bjoern Gruening 

Hi Philipp,

have you followed this from the readme?

Note that if you would like to run any of thecleanup scripts 
, 
you will need to add the following 
to|/export/galaxy-central/config/galaxy.ini|:


|database_connection = postgresql://galaxy:galaxy@localhost:5432/galaxy
file_path = /export/galaxy-central/database/files|

Or is this broken?
Cheers,
Bjoern


On 14.06.2016 09:21, Rathert, Philipp, Dr. wrote:

cleanup datasets error

Dear all,


when I want to start the cleanup datasets script I get the following 
error.



(.venv)root@galaxy:/galaxy-central# python 
/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py 
config/galaxy.ini -d -10 -1


Traceback (most recent call last):

  File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", 
line 544, in 


main()

  File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", 
line 99, in main


for key, value in config_parser.items( "app:main" ):

  File "/usr/lib/python2.7/ConfigParser.py", line 642, in items

raise NoSectionError(section)

ConfigParser.NoSectionError: No section: 'app:main'



We are using the docker galaxy stable 16.04 version. Before this 
script always worked without producing any error.



It would be great if anybody has an idea how to fix this...


Thank you very much in advance.


Cheers,


Philipp



-Original message-
*From:* Marius van den Beek 
*Sent:* Tuesday 7th June 2016 14:06
*To:* Marco Tangaro 
*Cc:* galaxy-dev 
*Subject:* Re: [galaxy-dev] Python tool wrapper with multiple input 
and output files


Hi Marco,

you've got an interesting use-case there.
You may want to use either a dataset list (if you only supply rna_n.bam),
or a paired dataset list (rna_n.bam and dna_n.bam).
I would probably implement a conditional, where the user selects 
either a dataset list or a paired dataset list.

The output would then be another collection of output files.
Have a look at the test tool folder, and see if any of the tools named 
collection_*.xml fits what you would like to do

https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools
These two may be a good basis for what you want to achieve:
https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_creates_list.xml
[this one creates an output collection]
https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_two_paired.xml
[this one has a conditional to either select a list or a paired list 
as input]


Let us know if you need more help!

Cheers,
Marius

On 7 June 2016 at 09:50, Marco Tangaro > wrote:

Dear experts,
my name is Marco and I'm working to port our python tool to the Galaxy 
framework.
The main script needs a rna.bam file as input, a reference fasta file, 
both mandatory. Finally, you can add a dna.bam file, but this is optional.

Therefore an example command is:

script.py -i rna.bam -f reference.fa -j dna.bam

The outout is a tabular.
Again the -j dna.bam option is completely optional.
So quite soon it turned out that I had to use a python wrapper to 
parse our script. Now the wrapper works fine.



The next step is to run the tool over multiple input file and we would 
like to avoid to use a workflow.


The idea is that to each input file corresponds an output file. The 
reference is still the same.

For instance, we have:

rna_1.bam + dna_1.bam -> output_1.txt
rna_2.bam + dna_2.bam -> output_2.txt
rna_3.bam + dna_3.bam -> output_3.txt
...
and so on.


But I don't know the best strategy to give to my wrapper multiple 
input files.
Moreover I have to be sure, when the dna_xyz.bam files are uploaded, 
that they correspond to the right rna_xyz.bam file.


I would like to have as output a page which is showing as results the 
link to the single output files as suggested here.

https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
planning to integrate a javascript interface.

I've browsed a lot, but on multiple input file the posts are old.
I'm using the last galaxy release (16_04).

I'm quite new to the galaxy world...
Thanks a lot for your suggestions,
Marco

___
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:
https://lists.galaxyproject.org/

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___
Please keep all replies on the list by using "reply all"
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and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/

[galaxy-dev] cleanup datasets error

2016-06-14 Thread Rathert , Philipp , Dr . 
Dear all,



when I want to start the cleanup datasets script I get the following error.



(.venv)root@galaxy:/galaxy-central# python 
/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini 
-d -10 -1

Traceback (most recent call last):

  File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", line 
544, in 

    main()

  File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", line 99, 
in main

    for key, value in config_parser.items( "app:main" ):

  File "/usr/lib/python2.7/ConfigParser.py", line 642, in items

    raise NoSectionError(section)

ConfigParser.NoSectionError: No section: 'app:main'






We are using the docker galaxy stable 16.04 version. Before this script always 
worked without producing any error. 



It would be great if anybody has an idea how to fix this...



Thank you very much in advance.



Cheers,



Philipp 





-Original message-
From: Marius van den Beek 
Sent: Tuesday 7th June 2016 14:06
To: Marco Tangaro 
Cc: galaxy-dev 
Subject: Re: [galaxy-dev] Python tool wrapper with multiple input and 
outputfiles


Hi Marco,

you've got an interesting use-case there.
You may want to use either a dataset list (if you only supply rna_n.bam),
or a paired dataset list (rna_n.bam and dna_n.bam). 
I would probably implement a conditional, where the user selects either a 
dataset list or a paired dataset list.
The output would then be another collection of output files.
Have a look at the test tool folder, and see if any of the tools named 
collection_*.xml fits what you would like to do
https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools
These two may be a good basis for what you want to achieve:
https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_creates_list.xml
[this one creates an output collection]
https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_two_paired.xml
[this one has a conditional to either select a list or a paired list as input]

Let us know if you need more help!

Cheers,
Marius

On 7 June 2016 at 09:50, Marco Tangaro mailto:ma.tang...@gmail.com> > wrote:
Dear experts,
my name is Marco and I'm working to port our python tool to the Galaxy 
framework.
The main script needs a rna.bam file as input, a reference fasta file, both 
mandatory. Finally, you can add a dna.bam file, but this is optional.
Therefore an example command is:

script.py -i rna.bam -f reference.fa -j dna.bam

The outout is a tabular.
Again the -j dna.bam option is completely optional.
So quite soon it turned out that I had to use a python wrapper to parse our 
script. Now the wrapper works fine.


The next step is to run the tool over multiple input file and we would like to 
avoid to use a workflow.

The idea is that to each input file corresponds an output file. The reference 
is still the same.
For instance, we have:

rna_1.bam + dna_1.bam -> output_1.txt
rna_2.bam + dna_2.bam -> output_2.txt
rna_3.bam + dna_3.bam -> output_3.txt
...
and so on.


But I don't know the best strategy to give to my wrapper multiple input files.
Moreover I have to be sure, when the dna_xyz.bam files are uploaded, that they 
correspond to the right rna_xyz.bam file.

I would like to have as output a page which is showing as results the link to 
the single output files as suggested here.
https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
planning to integrate a javascript interface.

I've browsed a lot, but on multiple input file the posts are old.
I'm using the last galaxy release (16_04).

I'm quite new to the galaxy world...
Thanks a lot for your suggestions,
Marco

___
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:
  https://lists.galaxyproject.org/

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


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

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