Re: [galaxy-dev] cloudman on private cloud

2011-10-11 Thread Enis Afgan 
Hi Rodrigo,
I'm currently working on support for Eucalyptus clouds, so if that's the
cloud infrastructure you have setup locally, support will be available soon.
However, it is not working yet.

Enis

2011/10/10 Rodrigo García Herrera 

> Hello!
>
> If I setup a private cloud infrastructure with ubuntu, can I setup galaxy
> cloudman there?
>
> Thanks!
>
> Rodrigo
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[galaxy-dev] strange history error

2011-10-11 Thread Chorny, Ilya 
I am getting a strange error that I cannot figure out how to debug. It's from a 
second instance we have running on the same server.  When I upload data it does 
not show me my history. I get the following messages from the log file. 
Thoughts?

galaxy.web.framework DEBUG 2011-10-11 15:47:50,259 Error: this request returned 
None from get_history(): 
http://ussd-dev-swim02.illumina.com/galaxy2/history/list
galaxy.web.framework DEBUG 2011-10-11 15:47:50,261 Error: this request returned 
None from get_history(): 
http://ussd-dev-swim02.illumina.com/galaxy2/history/list
galaxy.web.framework DEBUG 2011-10-11 16:34:25,717 Error: this request returned 
None from get_his tory(): 
http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create
galaxy.web.framework DEBUG 2011-10-11 16:34:25,717 Error: this request returned 
None from get_his tory(): 
http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create
galaxy.web.framework DEBUG 2011-10-11 16:34:25,718 Error: this request returned 
None from get_his tory(): 
http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create
galaxy.web.framework DEBUG 2011-10-11 16:34:25,718 Error: this request returned 
None from get_his tory(): 
http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create
galaxy.web.framework DEBUG 2011-10-11 16:34:25,718 Error: this request returned 
None from get_his tory(): 
http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create
galaxy.web.framework DEBUG 2011-10-11 16:34:25,718 Error: this request returned 
None from get_his tory(): 
http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create
galaxy.web.framework DEBUG 2011-10-11 16:34:25,719 Error: this request returned 
None from get_his tory(): 
http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create
galaxy.web.framework DEBUG 2011-10-11 16:34:25,719 Error: this request returned 
None from get_his tory(): 
http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create

Ilya Chorny Ph.D.
Bioinformatics Scientist I
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Work: 858.202.4582
Email: icho...@illumina.com
Website: www.illumina.com


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Re: [galaxy-dev] (i18n) How to make Galaxy display in Japanese?

2011-10-11 Thread Greg Von Kuster 
I don't think our locale support works with Cheetah, but  it's been quite some 
time since I've worked in this area, so I may be wrong. Most of the magic 
happens in the GalaxyWebTransaction.setup_i18n() method in 
~/lib/galaxy/web/framework.__init__.py which is mako centric.  It shouldn't be 
too difficult to add support for Cheetah templates if it's needed.  

The developers at the Database Center for the Life Science (DBCLS) in Japan 
host their own Galaxy instance (http://preview.galaxy.dbcls.jp/), and have done 
some work in this area, but a brief review of their tools does not show any 
that display Japanese.

Greg Von Kuster

On Oct 10, 2011, at 10:01 PM, Hanfei Sun wrote:

> It works when I set Japanese as the preferred language.
> 
> I saw these lines in ginga.po under the folder 
> galaxy-dist/locale/jp/LC_MESSAGES
> 
> #: tools/**.xml
> #: tool_conf.xml
> 
> msgid "Get Data"
> msgstr "データ取得"
> 
> msgid "Get ENCODE Data"
> msgstr "ENCODEデータ取得"
> 
> msgid "ENCODE Tools"
> msgstr "ENCODEツール"
> 
> But it seems that it doesn't have any effects (See screenshots).
> 
> Is it possible to make the text in xml files display in Japanese?
> 
> On 11-10-10 下午9:39, Greg Von Kuster wrote:
>> To clarify a bit more, there are currently only 2 languages supported in the
>> Galaxy distribution; English and Japanese (note the 'en' and 'ja' 
>> subdirectories
>> in the 'locale' directory). Setting your preferred language in your browser 
>> to
>> Japanese will only render some Galaxy content in Japanese. The strings that 
>> are
>> rendered in the preferred language (other than English) are preceded by an
>> underscore character and are enclosed in parentheses.
>> 
>> For example, in the Edit Attributes page for datasets, the following:
>> 
>> 
>> ${_('Edit Attributes')}
>> 
>> will render the section title in Japanese characters if that is your 
>> preferred
>> browser language encoding:
>> 
>> 
>> 
>> 
>> For example,
>> On Oct 10, 2011, at 9:26 AM, Daniel Blankenberg wrote:
>> 
>> >  Hi HF,
>> >
>> >  Limited support is available. In order to view Galaxy in other languages, 
>> > you
>> >  need to set the language preference in your browser to e.g. Japanese. 
>> > Chrom,
>> >  for example, allows you to set up a priority ordered list of prefered
>> >  languages, so you'll have to set Japanese to the top of the list for it to
>> >  request that language over English. Please let us know if you encounter
>> >  difficulties.
>> >
>> >
>> >  Thanks for using Galaxy,
>> >
>> >  Dan
>> >
>> >
>> >  On Oct 9, 2011, at 10:07 PM, 孙翰菲 wrote:
>> >
>> >>  Hi,all
>> >>
>> >>  I'm trying to translate galaxy into Chinese recently.
>> >>
>> >>  I found there's a directory "locale" under the galaxy directory, it looks
>> >>  like this:
>> >>
>> >>  .
>> >>  |-- en
>> >>  | `-- LC_MESSAGES
>> >>  | |-- ginga.mo
>> >>  | |-- ginga.po
>> >>  | |-- tools.mo
>> >>  | `-- tools.po
>> >>  |-- ginga.pot
>> >>  |-- ja
>> >>  | `-- LC_MESSAGES
>> >>  | |-- ginga.mo
>> >>  | |-- ginga.po
>> >>  | |-- tools.mo
>> >>  | `-- tools.po
>> >>  |-- tools.pot
>> >>
>> >>  It seems that Galaxy could display in Japanese, then I stopped the 
>> >> running
>> >>  galaxy service on the localhost and tried:
>> >>
>> >>  # export LANG=ja_JP.utf-8
>> >>  # run.sh
>> >>
>> >>  But the webpage is still English.
>> >>
>> >>  Then I copied the *.mo files to /usr/share/locale/ja_JP/LC_MESSAGES, but 
>> >> it
>> >>  doesn't work either.
>> >>
>> >>  Does anyone know whether it's possible to display galaxy in Japanese now?
>> >>
>> >>  Thanks!
>> >>
>> >>  HF
>> 
> 
>  上午09.55.20.png>___
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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu



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Re: [galaxy-dev] Possible to browse local filesystem

2011-10-11 Thread Greg Von Kuster 
Hello Alessandro,

You can upload files from filesystem paths to a Galaxy data library without 
copying the files into Galaxy's configured file directory.  This approach 
should provide what you're looking to do.  See our wiki at 
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files 
for all of the details.

Greg Von Kuster

On Oct 11, 2011, at 6:45 AM, alessandro albiero wrote:

> Dear all,
> 
> I have a problem with galaxy and I have already tried to write on ther user 
> list
> My problem concern the upload on galaxy of new files.
> 
> We are setting up a galaxy istance on our server (HPC Cluster with torque and 
> PBS) for internal use.
> Our problem is that we manage only NGS data (SOLiD and Illumina Data) that 
> are already stored on the server. 
> We tried to set up the user directory in the universe_wgsi.ini file to allow 
> to any user tu upload their local files, but adding new file and re-uploading 
> the dir we found duplicated files (it seems that galaxy re-upload every time 
> all the files ignoring if some are already present). This method is OK for us 
> but how can we avoid the file duplications ?
> 
> In a presentation found on web (blankenberg_pittsburg_2001), we saw that 
> there is the possibility to automatically upload the sequenced reads on 
> Galaxy (and let them available to all our user). Where can we find 
> information for doing this ?
> 
> 
> Thank in advance
> 
> All the best 
> 
> Alessandro 
> 
> 
> 
> 
> --
> **
> Alessandro Albiero
> Bioinformatics Lab
> CRIBI-Padua University
> Viale G. Colombo, 3
> 35121 Padova-Italy
> 
> http://genomics.cribi.unipd.it
> http://genomics.cribi.unipd.it/index.php/User:Albiero
> Phone. +39. 049 827-6165
> Fax.   +39. 049 827-6159
> 
> 
> 
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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu



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[galaxy-dev] Possible to browse local filesystem

2011-10-11 Thread alessandro albiero 
Dear all,

I have a problem with galaxy and I have already tried to write on ther user
list
My problem concern the upload on galaxy of new files.

We are setting up a galaxy istance on our server (HPC Cluster with torque
and PBS) for internal use.
Our problem is that we manage only NGS data (SOLiD and Illumina Data) that
are already stored on the server.
We tried to set up the user directory in the universe_wgsi.ini file to allow
to any user tu upload their local files, but adding new file and
re-uploading the dir we found duplicated files (it seems that galaxy
re-upload every time all the files ignoring if some are already present).
This method is OK for us but how can we avoid the file duplications ?

In a presentation found on web (blankenberg_pittsburg_2001), we saw that
there is the possibility to automatically upload the sequenced reads on
Galaxy (and let them available to all our user). Where can we find
information for doing this ?


Thank in advance

All the best

Alessandro




--
**
Alessandro Albiero
Bioinformatics Lab
CRIBI-Padua University
Viale G. Colombo, 3
35121 Padova-Italy

http://genomics.cribi.unipd.it
http://genomics.cribi.unipd.it/index.php/User:Albiero
Phone. +39. 049 827-6165
Fax.   +39. 049 827-6159

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