[galaxy-dev] organizing histories in galaxy

[Chaolin Zhang]

Hi,

Is there a way to organize related histories together into a "project" or 
folder?  

I realize in a lot of cases, a pipeline is designed for processing of a single 
sample, while a study typically consists of multiple samples that go through 
the same processing. They are then put together for more downstream analysis.  
It seems to me that it would be logical to put the processing of each 
individual file into a history, and the combined analysis into another, which 
would be bundled together.  I, and other users here have a growing list of 
histories, and it is becoming more and more difficult to organize them ...

Thanks!

Chaolin





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Re: [galaxy-dev] possible to undelete a history?

[Jennifer Jackson]

Hello Edward,

Have the user go into their account, use "Options -> Saved Histories" 
and click on "Advanced Search" at the top of the page. The refreshed 
page will have a link to view deleted histories "deleted: ". 
They can then check these and use the "undelete" button at the bottom of 
the page to restore them.


Sooner is better than later, depending on how often you purge/cleanup 
disc on your instance.


Hopefully this helps!

Jen

On 7/22/11 4:40 PM, Edward Kirton wrote:

An unfortunate user emailed me and said he accidentally deleted his
histories. :((
How can I help him recover these?



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--
Jennifer Jackson
http://usegalaxy.org/
http://galaxyproject.org/
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[galaxy-dev] possible to undelete a history?

[Edward Kirton]

An unfortunate user emailed me and said he accidentally deleted his
histories. :((
How can I help him recover these?
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Re: [galaxy-dev] Apache Configuration for Exporting Histories and Workflows

[Assaf Gordon]

Hi John,

John Chilton wrote, On 07/22/2011 11:40 AM:
> We have Galaxy behind an apache proxy, and apache is taking care of
> the authentication. If I want to enable exporting workflows and
> histories to other galaxy instances do I just need to disable the
> authentication checks for locations "/history/export_archive" and
> "/workflow/for_direct_import"? I assume this wouldn't also open a
> hole that would allow unpublished workflows or histories to be
> accessed by others (at my institution or else wise), is this
> correct?


We have the same situation with two internal galaxies. We use the following 
apache "mod_rewrite" rule to detect incoming requests from one galaxy server, 
and add a fake REMOTE_USER variable, simulating an authenticated user:

=
## This rule match "genomics.cshl.edu" server, and
## adds a fake authenticated user - allow people
## to copy datasets from rave to genomics
RewriteCond %{REMOTE_HOST}  =143.48.36.4
RewriteRule (.*) $1 [E=MCAC_UserName:genomics_import]


RequestHeader add REMOTE_USER %{MCAC_UserName}e

require valid-user
Order Allow,Deny
Allow from genomics.cshl.edu
Satisfy any


==

There are two important statements here:
1. the "RewriteCond + RewriteRule" check for the server's IP, and creates the 
environment variable for the fake authenticated user.
2. the "Allow from genomics" + "Satisfy any" means that apache will allow 
access to the "/galaxy" location from either an authenticated user or from a 
specific host.

Hope this helps,
 -gordon



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Re: [galaxy-dev] Upload of images - jpg/png - "binary file contains inappropriate content"

[Greg Von Kuster]

Based on the error message you gave, I assume the following code in 
~/lib/galaxy/datatypes/sniff.py is presenting the problem.

if check_binary( filename ):
if ext not in unsniffable_binary_formats and not 
datatypes_registry.get_datatype_by_extension( ext ).sniff( filename ):
raise InappropriateDatasetContentError, 'The binary uploaded file 
contains inappropriate content.'

Have you tried adding your 'jpg' extension to the following in 
~/lib/galaxy/datatypes/binary.py?

# Currently these supported binary data types must be manually set on upload
unsniffable_binary_formats = [ 'ab1', 'scf' ]


On Jul 22, 2011, at 11:52 AM, Jelle Scholtalbers wrote:

> Hi Greg,
> 
> I used that link when trying to create the support. The jpg datatype was 
> already present in the datatypes_conf.xml (
> 
>  mimetype="image/jpeg"/> )
> , so I first made it available at upload -> display_in_upload=True. As far as 
> I understood, if galaxy doesn't have to guess what the format is, this would 
> be sufficient? From step2:
> 
> "Galaxy tools are configured to automatically set the data type of an output 
> dataset. However, in some scenarios, Galaxy will attempt to determine the 
> data type of a file using a sniffer"
> 
> However manually setting the format on upload still gave the mentioned error. 
> Therefore I followed the rest of the guide (adding a sniffer) but still seem 
> to fail here..
> 
> Cheers,
> Jelle
> 
> 
> 
> On Jul 22, 2011 3:26 PM, "Greg Von Kuster"  wrote:
> > Hello Jelle,
> > 
> > There are a few things you need to do to add support for a new data type. 
> > The steps are described here:
> > 
> > http://wiki.g2.bx.psu.edu/Admin/Datatypes/Adding%20Datatypes
> > 
> > Greg Von Kuster
> > 
> > On Jul 22, 2011, at 8:49 AM, Jelle Scholtalbers wrote:
> > 
> >> Hi all,
> >> 
> >> I would like to be able to upload images to my Galaxy instance - in 
> >> particular jpg/png to data libraries. I can't however find out how to 
> >> overcome the problem of inappropriate content in binary file.
> >> How to go about? 
> >> 
> >> When I create a sniffer class in the galaxy.datatypes.images.py that 
> >> always returns true (for testing purposes) I still don't get the jpg 
> >> uploaded without an error (sniffer is incl. in the datatypes_conf.xml ). 
> >> class Jpg( Image ):
> >> file_ext = "jpg"
> >> def sniff(self, filename):
> >> """Determine if the file is in jpg format.
> >> """
> >> return True
> >> 
> >> It seems I'm missing something obvious and could use some help.
> >> 
> >> Cheers,
> >> Jelle
> >> ___
> >> 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/
> > 
> > Greg Von Kuster
> > Galaxy Development Team
> > g...@bx.psu.edu
> > 
> > 
> > 

Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu



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Re: [galaxy-dev] Newer Version of Cufflinks Wrapper

[Chorny, Ilya]

I just hit reply. Would be easier if when I hit reply it automatically sent the 
email back to the list. That's how other mailing lists that.I'm on work.

Thanks for the hg info.

Thanks,

Ilya

Sent from my iPhone

On Jul 22, 2011, at 6:32 AM, "Jeremy Goecks" 
mailto:jeremy.goe...@emory.edu>> wrote:

Ilya,

A patch is fine for a one-time fix; this is easy with Mercurial:

% hg diff > my_patch.patch

However, if you plan to contribute to Galaxy on a regular basis, we encourage 
you to fork Galaxy and maintain your own Bitbucket repository.

Finally, please send all emails to our mailing lists rather than individual 
Galaxy developers or other list members. Sending email to the mailing lists 
ensures that everyone can see and contribute to questions and issues; in 
addition, emails to mailing lists are tracked and archived so that they are 
available in the future.

Thanks,
J.


On Jul 21, 2011, at 5:16 PM, Chorny, Ilya wrote:

I would be happy to share any changes that I make. By patch do you mean a 
diff/patch share patch or just check in the code?

From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
Sent: Wednesday, July 20, 2011 4:55 PM
To: Chorny, Ilya
Cc:  
galaxy-user-boun...@lists.bx.psu.edu;
  
galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Newer Version of Cufflinks Wrapper

Ilya,

Despite the wrapper version numbers (which I'll update shortly to avoid further 
confusion), the current Cufflinks wrapper in both galaxy-central and 
galaxy-dist supports Cufflinks v1.0.3 However, not all new options for v1.0.3 
are implemented the current wrappers; should you decide to implement additional 
options in the Cufflinks/compare/diff wrappers, please consider submitting a 
patch that we could incorporate into Galaxy.

Best,
J.

On Jul 21, 2011, at 1:30 AM, Chorny, Ilya wrote:


Has anyone produced a newer version of the cufflinks wrapper? The current 
wrapper is for version 0.9.1.

Thanks,

Ilya



Ilya Chorny Ph.D.
Bioinformatics – Intern
icho...@illumina.com
858-202-4582

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Re: [galaxy-dev] Metadata in Galaxy Tool Shed

[Greg Von Kuster]

Hello Lance,

It looks like the repository metadata was successfully generated.  Normally 
this should take no more than a few seconds, but the server hosting our tool 
shed sometimes gets bogged down with other cpu intensive processes, so on some 
occasions, things don't work as expected.  We're working to resolve this 
problem.

Your choice for organizing the files looks good.

Thanks for sharing your tool on the tool shed, and let us know if you come 
across any other issues.

Greg Von Kuster

On Jul 22, 2011, at 11:37 AM, Lance Parsons wrote:

> I recently created a new repository in the galaxy tool shed for the cutadapt 
> tool and "imported" my old hg repository into it.  However, it doesn't seem 
> to be picking up the metadata correctly.  Does this take time, or is there 
> something I need to do to get the metadata generated correctly?  Also, any 
> suggestions on how to organize the files in the repository are welcome.  
> Thanks.
> 
> -- 
> Lance Parsons - Scientific Programmer
> 134 Carl C. Icahn Laboratory
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
> 
> ___
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> and other Galaxy lists, please use the interface at:
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>  http://lists.bx.psu.edu/

Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu




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Re: [galaxy-dev] new data type.

[Luobin Yang]

Hi, Hans,

Thanks for the link. I figured out the problem.  It turned out the data type
nexus was registered twice in the datatypes_conf.xml and the second one was
not using the right type.

THanks,
Luobin

On Fri, Jul 22, 2011 at 1:19 AM, Hans-Rudolf Hotz  wrote:

> Hi Luobin
>
> It is difficult to guess without seeing your code.
>
> So, assuming you followed the steps described in the wiki (
> http://wiki.g2.bx.psu.edu/**Admin/Datatypes/Adding%**20Datatypes),
> I guess you just made a typo somewhere (since this has happen to me several
> times when adding a new datatype). Have you double checked your tool
> definition file?
>
>
> Regards, Hans
>
>
>
> On 07/22/2011 07:52 AM, Luobin Yang wrote:
>
>> Hi,
>>
>> I created an XML file for a tool. This tool has an Nexus input. When I
>> click
>> the input field of the web interface for this tool, it shows all kinds of
>> data that I can select. How do I restrict the list to show only data in
>> nexus format? I added a line in the registration part and the sniffer part
>> of the datatypes_conf.xml and I also created a class called Nexus which
>> inherits the class galaxy.datatypes.Sequence, but this doesn't solve the
>> problem.
>>
>> Thanks,
>> Luobin
>>
>>
>>
>>
>> __**_
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>>   http://lists.bx.psu.edu/
>>
>
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Re: [galaxy-dev] Upload of images - jpg/png - "binary file contains inappropriate content"

[Jelle Scholtalbers]

Hi Greg,

I used that link when trying to create the support. The jpg datatype was
already present in the datatypes_conf.xml (

 )

, so I first made it available at upload -> display_in_upload=True. As far
as I understood, if galaxy doesn't have to guess what the format is, this
would be sufficient? From step2:

"Galaxy tools are configured to automatically set the data type of an output
dataset. However, in some scenarios, Galaxy will attempt to determine the
data type of a file using a sniffer"

However manually setting the format on upload still gave the mentioned
error. Therefore I followed the rest of the guide (adding a sniffer) but
still seem to fail here..

Cheers,
Jelle


On Jul 22, 2011 3:26 PM, "Greg Von Kuster"  wrote:
> Hello Jelle,
>
> There are a few things you need to do to add support for a new data type.
The steps are described here:
>
> http://wiki.g2.bx.psu.edu/Admin/Datatypes/Adding%20Datatypes
>
> Greg Von Kuster
>
> On Jul 22, 2011, at 8:49 AM, Jelle Scholtalbers wrote:
>
>> Hi all,
>>
>> I would like to be able to upload images to my Galaxy instance - in
particular jpg/png to data libraries. I can't however find out how to
overcome the problem of inappropriate content in binary file.
>> How to go about?
>>
>> When I create a sniffer class in the galaxy.datatypes.images.py that
always returns true (for testing purposes) I still don't get the jpg
uploaded without an error (sniffer is incl. in the datatypes_conf.xml ).
>> class Jpg( Image ):
>> file_ext = "jpg"
>> def sniff(self, filename):
>> """Determine if the file is in jpg format.
>> """
>> return True
>>
>> It seems I'm missing something obvious and could use some help.
>>
>> Cheers,
>> Jelle
>> ___
>> 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/
>
> Greg Von Kuster
> Galaxy Development Team
> g...@bx.psu.edu
>
>
>
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[galaxy-dev] Metadata in Galaxy Tool Shed

[Lance Parsons]

I recently created a new repository in the galaxy tool shed for the 
cutadapt tool and "imported" my old hg repository into it.  However, it 
doesn't seem to be picking up the metadata correctly.  Does this take 
time, or is there something I need to do to get the metadata generated 
correctly?  Also, any suggestions on how to organize the files in the 
repository are welcome.  Thanks.


--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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[galaxy-dev] Apache Configuration for Exporting Histories and Workflows

[John Chilton]

Hello All,

We have Galaxy behind an apache proxy, and apache is taking care of 
the authentication. If I want to enable exporting workflows and 
histories to other galaxy instances do I just need to disable the 
authentication checks for locations "/history/export_archive" and 
"/workflow/for_direct_import"? I assume this wouldn't also open a hole 
that would allow unpublished workflows or histories to be accessed by 
others (at my institution or else wise), is this correct?


Thanks for your time,
-John


John Chilton
Software Developer
University of Minnesota Supercomputing Institute
Office: 612-625-0917
Cell: 612-226-9223
E-Mail: chil...@msi.umn.edu

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[galaxy-dev] Scroll bars not present using i.e.

[Chorny, Ilya]

http://test.g2.bx.psu.edu/

Cheers,

Ilya

Ilya Chorny Ph.D.
Bioinformatics - Intern
icho...@illumina.com
858-202-4582

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Re: [galaxy-dev] error reading tool from path (epigraph.xml, epigraph_test.xml, access_libraries.xml)

[Greg Von Kuster]

This is due to a bug that was corrected in change set 5819:0f15591f2acd, which 
should be available in our main Galaxy instance, as well as the distribution, 
within the next few weeks.  If you need it sooner, you can pull it from our 
development repo.  Sorry for the inconvenience.

Greg Von Kuster

On Jul 22, 2011, at 11:00 AM, Leon Mei wrote:

> Dear all,
> 
> I installed a local galaxy using the latest codebase yesterday. During the 
> startup, the loading of 3 tool wrappers are failed: epigraph.xml, 
> epigraph_test.xml, access_libraries.xml.
> 
> Similar errors were reported in 
> http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg01839.html
> 
> Have other people experienced the same problem? Any suggested solutions?
> 
> Thanks,
> Leon
> 
>  paster.log below ===
> ...
> galaxy.tools DEBUG 2011-07-22 16:02:47,084 Loaded tool: hbvar 1.0.0
> galaxy.tools DEBUG 2011-07-22 16:02:47,088 Loaded tool: fix_errors 1.0.0
> galaxy.tools DEBUG 2011-07-22 16:02:47,089 Loading section: Send Data
> galaxy.tools ERROR 2011-07-22 16:02:47,089 error reading tool from path: 
> data_destination/epigraph.xml
> Traceback (most recent call last):
>   File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 
> 77, in load_tool
> tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
>   File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 
> 169, in load_tool
> return ToolClass( config_file, root, self.app )
>   File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 
> 340, in __init__
> self.parse( root )
>   File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 
> 385, in parse
> self.interpreter = command.get("interpreter", None)
> AttributeError: 'NoneType' object has no attribute 'get'
> galaxy.tools ERROR 2011-07-22 16:02:47,090 error reading tool from path: 
> data_destination/epigraph_test.xml
> Traceback (most recent call last):
>   File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 
> 77, in load_tool
> tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
>   File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 
> 169, in load_tool
> return ToolClass( config_file, root, self.app )
>   File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 
> 340, in __init__
> self.parse( root )
>   File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 
> 385, in parse
> self.interpreter = command.get("interpreter", None)
> AttributeError: 'NoneType' object has no attribute 'get'
> ...
> galaxy.tools DEBUG 2011-07-22 16:02:50,556 Loading section: SNP/WGA: Data; 
> Filters
> galaxy.tools DEBUG 2011-07-22 16:02:50,587 Loaded tool: upload1 1.1.3
> galaxy.tools ERROR 2011-07-22 16:02:50,587 error reading tool from path: 
> data_source/access_libraries.xml
> Traceback (most recent call last):
>   File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 
> 77, in load_tool
> tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
>   File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 
> 169, in load_tool
> return ToolClass( config_file, root, self.app )
>   File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 
> 340, in __init__
> self.parse( root )
>   File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 
> 385, in parse
> self.interpreter = command.get("interpreter", None)
> AttributeError: 'NoneType' object has no attribute 'get'
> ...
> 
> 
> -- 
> Hailiang (Leon) Mei
> Netherlands Bioinformatics Center (http://www.nbic.nl/)
> Skype: leon_meiMobile: +31 6 41709231
> ___
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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu



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Re: [galaxy-dev] Where to find the toolconfig parser code?

[Samuel Lampa]

On 07/22/2011 04:53 PM, Peter Cock wrote:

On Fri, Jul 22, 2011 at 3:50 PM, Samuel Lampa
  wrote:

The #if#else syntax, in for example this tool example:



... is that something that you galaxy parses itself (tried to grep for some
matching-code, but found nothing so far), or are that some python
preprocessor directives?


It is a Python template language called Cheetah, see for eg:
http://www.cheetahtemplate.org/docs/users_guide_html/

Peter


Ah, IC, big thanks! :)

// Samuel


--
System Expert / Bioinformatician
SNIC-UPPMAX / SciLifeLab Uppsala
Uppsala University, Sweden
--
E-mail: samuel.la...@scilifelab.uu.se
Phone: +46 (0)18 - 471 1060
WWW: http://www.uppmax.uu.se
Uppnex: https://www.uppnex.uu.se

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[galaxy-dev] error reading tool from path (epigraph.xml, epigraph_test.xml, access_libraries.xml)

[Leon Mei]

Dear all,

I installed a local galaxy using the latest codebase yesterday. During the
startup, the loading of 3 tool wrappers are failed: epigraph.xml,
epigraph_test.xml, access_libraries.xml.

Similar errors were reported in
http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg01839.html

Have other people experienced the same problem? Any suggested solutions?

Thanks,
Leon

 paster.log below ===
...
galaxy.tools DEBUG 2011-07-22 16:02:47,084 Loaded tool: hbvar 1.0.0
galaxy.tools DEBUG 2011-07-22 16:02:47,088 Loaded tool: fix_errors 1.0.0
galaxy.tools DEBUG 2011-07-22 16:02:47,089 Loading section: Send Data
galaxy.tools ERROR 2011-07-22 16:02:47,089 error reading tool from path:
data_destination/epigraph.xml
Traceback (most recent call last):
  File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py",
line 77, in load_tool
tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
  File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py",
line 169, in load_tool
return ToolClass( config_file, root, self.app )
  File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py",
line 340, in __init__
self.parse( root )
  File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py",
line 385, in parse
self.interpreter = command.get("interpreter", None)
AttributeError: 'NoneType' object has no attribute 'get'
galaxy.tools ERROR 2011-07-22 16:02:47,090 error reading tool from path:
data_destination/epigraph_test.xml
Traceback (most recent call last):
  File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py",
line 77, in load_tool
tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
  File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py",
line 169, in load_tool
return ToolClass( config_file, root, self.app )
  File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py",
line 340, in __init__
self.parse( root )
  File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py",
line 385, in parse
self.interpreter = command.get("interpreter", None)
AttributeError: 'NoneType' object has no attribute 'get'
...
galaxy.tools DEBUG 2011-07-22 16:02:50,556 Loading section: SNP/WGA: Data;
Filters
galaxy.tools DEBUG 2011-07-22 16:02:50,587 Loaded tool: upload1 1.1.3
galaxy.tools ERROR 2011-07-22 16:02:50,587 error reading tool from path:
data_source/access_libraries.xml
Traceback (most recent call last):
  File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py",
line 77, in load_tool
tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
  File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py",
line 169, in load_tool
return ToolClass( config_file, root, self.app )
  File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py",
line 340, in __init__
self.parse( root )
  File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py",
line 385, in parse
self.interpreter = command.get("interpreter", None)
AttributeError: 'NoneType' object has no attribute 'get'
...


-- 
Hailiang (Leon) Mei
Netherlands Bioinformatics Center (http://www.nbic.nl/)
Skype: leon_meiMobile: +31 6 41709231
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Re: [galaxy-dev] Where to find the toolconfig parser code?

[Peter Cock]

On Fri, Jul 22, 2011 at 3:50 PM, Samuel Lampa
 wrote:
> One follow up question then:
>
> The #if#else syntax, in for example this tool example:
>
>  ...
>
> ... is that something that you galaxy parses itself (tried to grep for some
> matching-code, but found nothing so far), or are that some python
> preprocessor directives?
>
> Best
> // Samuel

It is a Python template language called Cheetah, see for eg:
http://www.cheetahtemplate.org/docs/users_guide_html/

Peter

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Re: [galaxy-dev] Where to find the toolconfig parser code?

[Samuel Lampa]

One follow up question then:

The #if#else syntax, in for example this tool example:

  ...
  
sam_to_bam.py
  --input1=$source.input1
  --dbkey=${input1.metadata.dbkey}
  #if $source.index_source == "history":
--ref_file=$source.ref_file
  #else
--ref_file="None"
  #end if
  --output1=$output1
  --index_dir=${GALAXY_DATA_INDEX_DIR}
  
  
  ...

... is that something that you galaxy parses itself (tried to grep for 
some matching-code, but found nothing so far), or are that some python 
preprocessor directives?


Best
// Samuel


On 07/22/2011 04:45 PM, Samuel Lampa wrote:

Ah, thanks!  I somehow missed that file altogether ...

// Samuel

On 07/22/2011 03:59 PM, Greg Von Kuster wrote:

Samuel,

Look at the parse(0 method in the Tool class in 
~/lib/galaxy/tools/__init__.py for most of it.  You should be able to 
find everything you need from there.


Greg Von Kuster

On Jul 22, 2011, at 9:41 AM, Samuel Lampa wrote:


Quick question to you devs,

I need to find the code where the tool configs are parsed ... 
especially the "free-text" if-else clauses in the command-tag.


Could someone point me to the file?

TIA
// Samuel

--
System Expert / Bioinformatician
SNIC-UPPMAX / SciLifeLab Uppsala
Uppsala University, Sweden
--
E-mail: samuel.la...@scilifelab.uu.se
Phone: +46 (0)18 - 471 1060
WWW: http://www.uppmax.uu.se
Uppnex: https://www.uppnex.uu.se

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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu










--
System Expert / Bioinformatician
SNIC-UPPMAX / SciLifeLab Uppsala
Uppsala University, Sweden
--
E-mail: samuel.la...@scilifelab.uu.se
Phone: +46 (0)18 - 471 1060
WWW: http://www.uppmax.uu.se
Uppnex: https://www.uppnex.uu.se

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Re: [galaxy-dev] Where to find the toolconfig parser code?

[Samuel Lampa]

Ah, thanks!  I somehow missed that file altogether ...

// Samuel

On 07/22/2011 03:59 PM, Greg Von Kuster wrote:

Samuel,

Look at the parse(0 method in the Tool class in ~/lib/galaxy/tools/__init__.py 
for most of it.  You should be able to find everything you need from there.

Greg Von Kuster

On Jul 22, 2011, at 9:41 AM, Samuel Lampa wrote:


Quick question to you devs,

I need to find the code where the tool configs are parsed ... especially the 
"free-text" if-else clauses in the command-tag.

Could someone point me to the file?

TIA
// Samuel

--
System Expert / Bioinformatician
SNIC-UPPMAX / SciLifeLab Uppsala
Uppsala University, Sweden
--
E-mail: samuel.la...@scilifelab.uu.se
Phone: +46 (0)18 - 471 1060
WWW: http://www.uppmax.uu.se
Uppnex: https://www.uppnex.uu.se

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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu







--
System Expert / Bioinformatician
SNIC-UPPMAX / SciLifeLab Uppsala
Uppsala University, Sweden
--
E-mail: samuel.la...@scilifelab.uu.se
Phone: +46 (0)18 - 471 1060
WWW: http://www.uppmax.uu.se
Uppnex: https://www.uppnex.uu.se

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Re: [galaxy-dev] Error moving tool-data dir ... bowite indexes missing

[Bossers, Alex]

Ross,

I think I don't understand what you mean. Do you mean the actual reference to 
the files contained in the loc file?
I have all non-relative paths to the bowtie indexes (snippet below). The last 
column is an additional column for some plotting tools to have a sensible short 
name and works fine in the original location.
Separators are tabs.

Alex {still confused}
==
Part of the bowtie_indices.loc
--
Bos_taurus_ensembl  Bos_taurus_ensembl  Bos taurus ensembl 4.0.61   
/share/bowtie/indexes/Bos_taurus_ensemblBosTaurus
Homo_sapiens.GRCh37 Homo_sapiens.GRCh37 Homo sapiens ensembl GRch37 
/share/bowtie/indexes/Homo_sapiens.GRCh37   Human
Macaca_mulatta_NCBIdraft20110405Macaca_mulatta_NCBIdraft20110405
Macaca mulatta (rhesus monkey draft NCBI)   
/share/bowtie/indexes/Macaca_mulatta_NCBIdraft20110405  Macaca
Mus_musculus.NCBIM37Mus_musculus.NCBIM37Mus musculus NCBIM37
/share/bowtie/indexes/Mus_musculus.NCBIM37  Mouse
--


-Oorspronkelijk bericht-
Van: Ross [mailto:ross.laza...@gmail.com]
Verzonden: vrijdag 22 juli 2011 15:15
Aan: Bossers, Alex
Onderwerp: Re: [galaxy-dev] Error moving tool-data dir ... bowite indexes 
missing

If those changes invalidate your loc files, you may need to adjust them?

On Fri, Jul 22, 2011 at 11:02 PM, Bossers, Alex 
mailto:alex.boss...@wur.nl>> wrote:
> On our up-to-date galaxy_central version I have successfully moved the
> database/files directory to mounted storage. After adapting the
> universe_wsgi.ini it works fine after galaxy restart.
>
>
>
> Now the tool-data dir becomes bigger and bigger and I wanted to move
> that to mounted storage as well.
>
> I moved the tool-data dir to the other location, made sure file
> permissions were ok and adapted the universe_wsgi.ini tool_data_path
> to match the new tool-data location.
>
>
>
> Galaxy restarts and the loc files are read (since blast recognises its
> databases). However, the bowtie indexes are not read since they do not
> show up in the NGS bowtie mapper for illumina. what could be wrong?
>
>
>
> When I restore the universe_wsgi.ini it works all fine.
>
> I am puzzled.
>
>
>
>
>
> Alex
>
>
>
>
>
>
>
>
>
> ___
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> Galaxy lists, please use the interface at:
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>  http://lists.bx.psu.edu/
>



--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School; Director of Bioinformatics, 
Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; 
Tel: +61 385321444;


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Re: [galaxy-dev] Where to find the toolconfig parser code?

[Greg Von Kuster]

Samuel,

Look at the parse(0 method in the Tool class in ~/lib/galaxy/tools/__init__.py 
for most of it.  You should be able to find everything you need from there.

Greg Von Kuster

On Jul 22, 2011, at 9:41 AM, Samuel Lampa wrote:

> Quick question to you devs,
> 
> I need to find the code where the tool configs are parsed ... especially the 
> "free-text" if-else clauses in the command-tag.
> 
> Could someone point me to the file?
> 
> TIA
> // Samuel
> 
> -- 
> System Expert / Bioinformatician
> SNIC-UPPMAX / SciLifeLab Uppsala
> Uppsala University, Sweden
> --
> E-mail: samuel.la...@scilifelab.uu.se
> Phone: +46 (0)18 - 471 1060
> WWW: http://www.uppmax.uu.se
> Uppnex: https://www.uppnex.uu.se
> 
> ___
> 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/

Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu




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[galaxy-dev] Where to find the toolconfig parser code?

[Samuel Lampa]

Quick question to you devs,

I need to find the code where the tool configs are parsed ... especially 
the "free-text" if-else clauses in the command-tag.


Could someone point me to the file?

TIA
// Samuel

--
System Expert / Bioinformatician
SNIC-UPPMAX / SciLifeLab Uppsala
Uppsala University, Sweden
--
E-mail: samuel.la...@scilifelab.uu.se
Phone: +46 (0)18 - 471 1060
WWW: http://www.uppmax.uu.se
Uppnex: https://www.uppnex.uu.se

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Re: [galaxy-dev] Newer Version of Cufflinks Wrapper

[Jeremy Goecks]

Ilya,

A patch is fine for a one-time fix; this is easy with Mercurial: 

% hg diff > my_patch.patch 

However, if you plan to contribute to Galaxy on a regular basis, we encourage 
you to fork Galaxy and maintain your own Bitbucket repository.

Finally, please send all emails to our mailing lists rather than individual 
Galaxy developers or other list members. Sending email to the mailing lists 
ensures that everyone can see and contribute to questions and issues; in 
addition, emails to mailing lists are tracked and archived so that they are 
available in the future.

Thanks,
J.


On Jul 21, 2011, at 5:16 PM, Chorny, Ilya wrote:

> I would be happy to share any changes that I make. By patch do you mean a 
> diff/patch share patch or just check in the code?
>  
> From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] 
> Sent: Wednesday, July 20, 2011 4:55 PM
> To: Chorny, Ilya
> Cc: galaxy-user-boun...@lists.bx.psu.edu; galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] Newer Version of Cufflinks Wrapper
>  
> Ilya,
>  
> Despite the wrapper version numbers (which I'll update shortly to avoid 
> further confusion), the current Cufflinks wrapper in both galaxy-central and 
> galaxy-dist supports Cufflinks v1.0.3 However, not all new options for v1.0.3 
> are implemented the current wrappers; should you decide to implement 
> additional options in the Cufflinks/compare/diff wrappers, please consider 
> submitting a patch that we could incorporate into Galaxy.
>  
> Best,
> J.
>  
> On Jul 21, 2011, at 1:30 AM, Chorny, Ilya wrote:
> 
> 
> Has anyone produced a newer version of the cufflinks wrapper? The current 
> wrapper is for version 0.9.1.
>  
> Thanks,
>  
> Ilya
>  
>  
>  
> Ilya Chorny Ph.D.
> Bioinformatics – Intern
> icho...@illumina.com
> 858-202-4582
>  
> ___
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> and other Galaxy lists, please use the interface at:
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>  http://lists.bx.psu.edu/
>  

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Re: [galaxy-dev] Upload of images - jpg/png - "binary file contains inappropriate content"

[Greg Von Kuster]

Hello Jelle,

There are a few things you need to do to add support for a new data type.  The 
steps are described here:

http://wiki.g2.bx.psu.edu/Admin/Datatypes/Adding%20Datatypes

Greg Von Kuster

On Jul 22, 2011, at 8:49 AM, Jelle Scholtalbers wrote:

> Hi all,
> 
> I would like to be able to upload images to my Galaxy instance - in 
> particular jpg/png to data libraries. I can't however find out how to 
> overcome the problem of inappropriate content in binary file.
> How to go about? 
> 
> When I create a sniffer class in the galaxy.datatypes.images.py that always 
> returns true (for testing purposes) I still don't get the jpg uploaded 
> without an error (sniffer is incl. in the datatypes_conf.xml ). 
> class Jpg( Image ):
> file_ext = "jpg"
> def sniff(self, filename):
> """Determine if the file is in jpg format.
> """
> return True
> 
> It seems I'm missing something obvious and could use some help.
> 
> Cheers,
> Jelle
> ___
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> and other Galaxy lists, please use the interface at:
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>  http://lists.bx.psu.edu/

Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu



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[galaxy-dev] Error moving tool-data dir ... bowite indexes missing

[Bossers, Alex]

On our up-to-date galaxy_central version I have successfully moved the 
database/files directory to mounted storage. After adapting the 
universe_wsgi.ini it works fine after galaxy restart.

Now the tool-data dir becomes bigger and bigger and I wanted to move that to 
mounted storage as well.
I moved the tool-data dir to the other location, made sure file permissions 
were ok and adapted the universe_wsgi.ini tool_data_path to match the new 
tool-data location.

Galaxy restarts and the loc files are read (since blast recognises its 
databases). However, the bowtie indexes are not read since they do not show up 
in the NGS bowtie mapper for illumina. what could be wrong?

When I restore the universe_wsgi.ini it works all fine.
I am puzzled.


Alex




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[galaxy-dev] Upload of images - jpg/png - "binary file contains inappropriate content"

[Jelle Scholtalbers]

Hi all,

I would like to be able to upload images to my Galaxy instance - in
particular jpg/png to data libraries. I can't however find out how to
overcome the problem of inappropriate content in binary file.
How to go about?

When I create a sniffer class in the galaxy.datatypes.images.py that always
returns true (for testing purposes) I still don't get the jpg uploaded
without an error (sniffer is incl. in the datatypes_conf.xml ).
class Jpg( Image ):
file_ext = "jpg"
def sniff(self, filename):
"""Determine if the file is in jpg format.
"""
return True

It seems I'm missing something obvious and could use some help.

Cheers,
Jelle
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Re: [galaxy-dev] new data type.

[Hans-Rudolf Hotz]

Hi Luobin

It is difficult to guess without seeing your code.

So, assuming you followed the steps described in the wiki 
(http://wiki.g2.bx.psu.edu/Admin/Datatypes/Adding%20Datatypes), I guess 
you just made a typo somewhere (since this has happen to me several 
times when adding a new datatype). Have you double checked your tool 
definition file?



Regards, Hans


On 07/22/2011 07:52 AM, Luobin Yang wrote:

Hi,

I created an XML file for a tool. This tool has an Nexus input. When I click
the input field of the web interface for this tool, it shows all kinds of
data that I can select. How do I restrict the list to show only data in
nexus format? I added a line in the registration part and the sniffer part
of the datatypes_conf.xml and I also created a class called Nexus which
inherits the class galaxy.datatypes.Sequence, but this doesn't solve the
problem.

Thanks,
Luobin




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