Re: [galaxy-dev] renaming fastq to fastqsanger

[Peter Cock]

On Wednesday, October 3, 2012, Pete Schmitt wrote:

>
> When attempting the change the filetype of a fastq file to fastqsanger,
> the process for changing the type goes on forever.  This
> does not allow any further processing of the data.
>
>
That's strange - this should be really fast as it doesn't change the file
on disk, just the metadata in Galaxy's database.

(The FASTQ groomer is much slower because it does write a new file)

Which Galaxy installation was this on? If yours, do you know anything about
the setup (e.g. database used)?

Peter
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Re: [galaxy-dev] The blastdb_p.loc sample is wrong.

[Peter Cock]

On Thursday, October 4, 2012, Shane Sturrock wrote:

> Hi Peter,
>
> Thanks for the quick reply.
>

No problem.


> This section:
>
> #Your blastdb_p.loc file should include an entry per line for each "base
> name"
> #you have stored. For example:
> #
> #nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010
> /data/blastdb/05Jun2010/nr
> #nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010
> /data/blastdb/15Aug2010/nr
> #...etc...
> #
> #See also blastdb.loc which is for any nucleotide BLAST database.
>
> There are two tabs between the 2010 and /data
>

Sigh. I've been using emacs to edit these files on our server, and
it doesn't show non-printing characters like tabs in a visible way
(at least, not with the default settings - any tips?). Note I'm not
using xemacs, just the terminal based one. And typing a raw
tab involves a tedious control sequence... there probably is an
easier way, but I don't edit these loc files very often.

(Note that user defined BLAST databases are coming soon
to the BLAST+ wrappers, delayed by a hardware problem
on our local system meaning I haven't finished testing it)


>
> Like an idiot I just copied one of those lines and changed it to
>
match my local database setup and then spent literally hours
>
trying to figure out why blast from the command line worked
>
fine, but I couldn't get it to work with Galaxy.
>

Sorry about that - but by reporting this and getting it fixed you've
hopefully saved anyone else suffering this way.

I'm at a meeting all day so I probably won't be able to update
this till next week.

Peter
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[galaxy-dev] Mapping input fields in a workflow

[Lukasse, Pieter]

Hi,

Is there any way to map an input field from one tool to the input field of 
another tool in a workflow?

E.g. let's say tool A has an input field X which tool B also has. If we use 
both tool A and B in the same workflow, then we would like to let the user fill 
in field X only once in tool A and then map that value to the field X in tool 
B. As far as I can see, there is now only a way to map output files of tool A 
to input files of tool B.

[cid:image001.png@01CDA2E2.20BC4390]

Regards,

Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
+31-317480891; skype: pieter.lukasse.wur
http://www.pri.wur.nl

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[galaxy-dev] History import returns size zero

[Bossers, Alex]

Dear all,

I might have missed it on the list and cannot find it in the archive;

When we import a history exported from the same or another galaxy instance it 
imports ok and all files are there and usuable, only the history size is 0.
We are up to latest galaxy-central of October 4th.

Is this a bug (or some feature :-) ).

Alex




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[galaxy-dev] stack trace from a history problem

[Langhorst, Brad]

On one particular history, I see this.

I am at 
035583d94b11


I don't know why this happens on this history…
I cloned it, then re-ran one step.

I hope this stacktrace is helpful:

Exception happened during processing of request from ('127.0.0.1', 56949)
Traceback (most recent call last):
  File 
"/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", 
line 1053, in process_request_in_thread
self.finish_request(request, client_address)
  File "/usr/lib/python2.6/SocketServer.py", line 320, in finish_request
self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib/python2.6/SocketServer.py", line 615, in __init__
self.handle()
  File 
"/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", 
line 432, in handle
BaseHTTPRequestHandler.handle(self)
  File "/usr/lib/python2.6/BaseHTTPServer.py", line 329, in handle
self.handle_one_request()
  File 
"/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", 
line 427, in handle_one_request
self.wsgi_execute()
  File 
"/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", 
line 287, in wsgi_execute
self.wsgi_start_response)
  File 
"/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/urlmap.py", 
line 202, in __call__
return app(environ, start_response)
  File 
"/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/xforwardedhost.py",
 line 21, in __call__
return self.app( environ, start_response )
  File 
"/mnt/ngswork/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/config.py",
 line 164, in __call__
app_iter = self.application(environ, start_response)
  File 
"/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/translogger.py",
 line 68, in __call__
return self.application(environ, replacement_start_response)
  File 
"/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py",
 line 153, in __call__
exc_info)
  File 
"/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/translogger.py",
 line 67, in replacement_start_response
return start_response( status, headers, exc_info )
  File 
"/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py",
 line 143, in __call__
app_iter = self.application(environ, start_response)
  File 
"/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py", 
line 80, in __call__
return self.application(environ, start_response)
  File 
"/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py",
 line 91, in __call__
return self.app( environ, start_response )
  File 
"/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py",
 line 632, in __call__
return self.application(environ, start_response)
  File "/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py", line 
169, in __call__
return body( environ, start_response )
  File "/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py", 
line 858, in render
template.render_context( context )
  File 
"/mnt/ngswork/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py", 
line 319, in render_context
**kwargs)
  File 
"/mnt/ngswork/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py", 
line 692, in _render_context
_exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
  File 
"/mnt/ngswork/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py", 
line 718, in _exec_template
callable_(context, *args, **kwargs)
  File 
"/mnt/ngswork/galaxy/galaxy-dist/database/compiled_templates/root/history.mako.py",
 line 306, in render_body
__M_writer(unicode(render_dataset( data, data.hid, show_deleted_on_refresh 
= show_deleted, for_editing = True )))
  File 
"/mnt/ngswork/galaxy/galaxy-dist/database/compiled_templates/root/history_common.mako.py",
 line 553, in render_render_dataset
visualizations = data.get_visualizations()
  File "/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 
1251, in get_visualizations
return self.datatype.get_visualizations( self )
  File "/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/datatypes/tabular.py", line 
312, in get_visualizations
for col_type in dataset.metadata.column_types:
TypeError: 'NoneType' object is not iterable

brad
--
Brad Langhorst
langho...@neb.com





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Re: [galaxy-dev] stack trace from a history problem

[Jeremy Goecks]

That's a bug, fixed in cf93e8aa50f9

Thanks,
J.

On Oct 5, 2012, at 9:34 AM, Langhorst, Brad wrote:

> 
> On one particular history, I see this.
> 
> I am at 035583d94b11
> 
> 
> I don't know why this happens on this history…
> I cloned it, then re-ran one step.
> 
> I hope this stacktrace is helpful:
> 
> Exception happened during processing of request from ('127.0.0.1', 56949)
> Traceback (most recent call last):
>   File 
> "/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
>  line 1053, in process_request_in_thread
> self.finish_request(request, client_address)
>   File "/usr/lib/python2.6/SocketServer.py", line 320, in finish_request
> self.RequestHandlerClass(request, client_address, self)
>   File "/usr/lib/python2.6/SocketServer.py", line 615, in __init__
> self.handle()
>   File 
> "/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
>  line 432, in handle
> BaseHTTPRequestHandler.handle(self)
>   File "/usr/lib/python2.6/BaseHTTPServer.py", line 329, in handle
> self.handle_one_request()
>   File 
> "/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
>  line 427, in handle_one_request
> self.wsgi_execute()
>   File 
> "/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
>  line 287, in wsgi_execute
> self.wsgi_start_response)
>   File 
> "/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/urlmap.py", 
> line 202, in __call__
> return app(environ, start_response)
>   File 
> "/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/xforwardedhost.py",
>  line 21, in __call__
> return self.app( environ, start_response )
>   File 
> "/mnt/ngswork/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/config.py",
>  line 164, in __call__
> app_iter = self.application(environ, start_response)
>   File 
> "/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/translogger.py",
>  line 68, in __call__
> return self.application(environ, replacement_start_response)
>   File 
> "/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py",
>  line 153, in __call__
> exc_info)
>   File 
> "/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/translogger.py",
>  line 67, in replacement_start_response
> return start_response( status, headers, exc_info )
>   File 
> "/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py",
>  line 143, in __call__
> app_iter = self.application(environ, start_response)
>   File 
> "/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py",
>  line 80, in __call__
> return self.application(environ, start_response)
>   File 
> "/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py",
>  line 91, in __call__
> return self.app( environ, start_response )
>   File 
> "/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py",
>  line 632, in __call__
> return self.application(environ, start_response)
>   File "/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py", 
> line 169, in __call__
> return body( environ, start_response )
>   File 
> "/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py", line 
> 858, in render
> template.render_context( context )
>   File 
> "/mnt/ngswork/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py", 
> line 319, in render_context
> **kwargs)
>   File 
> "/mnt/ngswork/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py", 
> line 692, in _render_context
> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
>   File 
> "/mnt/ngswork/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py", 
> line 718, in _exec_template
> callable_(context, *args, **kwargs)
>   File 
> "/mnt/ngswork/galaxy/galaxy-dist/database/compiled_templates/root/history.mako.py",
>  line 306, in render_body
> __M_writer(unicode(render_dataset( data, data.hid, 
> show_deleted_on_refresh = show_deleted, for_editing = True )))
>   File 
> "/mnt/ngswork/galaxy/galaxy-dist/database/compiled_templates/root/history_common.mako.py",
>  line 553, in render_render_dataset
> visualizations = data.get_visualizations()
>   File "/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 
> 1251, in get_visualizations
> return self.datatype.get_visualizations( self )
>   File "/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/datatypes/tabular.py", 
> line 312, in get_visualizations
> for col_type in dataset.metadata.column_types:
> TypeError: 'NoneType' object is not iterable
> 
> brad
> --
> Brad Langhorst
> langho...@neb.com
> 
> 
> 
> 
> 
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[galaxy-dev] trying to set up local toolshed

[David Hoover]

I'm trying to host a local toolshed, and I've hit a brick wall.  It is 
accessible as a subdirectory under our galaxy installation, uses SQLite as the 
database, and I've configured it as much as I understand.  After I start it up, 
I can see the main page in the browser, but get this error message:

Not Found

The resource could not be found. 
No route for /repository/browse_categories

Clicking on 'Repositories' gives this error:

This link may not be followed from within Galaxy.

Beyond this, can the toolshed use externally authenticated users?

David Hoover
Helix Systems Staff
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[galaxy-dev] Instant crash on large history export

[Bossers, Alex]

Another problem;
On our ubuntu x64 server with the latest galaxy_central of Oct 4th...
An export of the history sized 2.5Gb was ok. However large exports (like 10Gb) 
make the server instantly crash (within a few seconds) without anything 
significant in the galaxy.log.
The apache server is still running though...

Help!
Alex




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Re: [galaxy-dev] trying to set up local toolshed

[Greg Von Kuster]

Hello David,

What version of Galaxy are you running?

Please send me your community_wsgi.ini file so I can take a look at how you 
have things configured.

Thanks,

Greg Von Kuster


On Oct 5, 2012, at 9:51 AM, David Hoover wrote:

> I'm trying to host a local toolshed, and I've hit a brick wall.  It is 
> accessible as a subdirectory under our galaxy installation, uses SQLite as 
> the database, and I've configured it as much as I understand.  After I start 
> it up, I can see the main page in the browser, but get this error message:
> 
> Not Found
> 
> The resource could not be found. 
> No route for /repository/browse_categories
> 
> Clicking on 'Repositories' gives this error:
> 
> This link may not be followed from within Galaxy.
> 
> Beyond this, can the toolshed use externally authenticated users?
> 
> David Hoover
> Helix Systems Staff
> ___
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[galaxy-dev] Workflow Batching Enhancements

[John Chilton]

Hello Galaxy People,

I have put together some batch workflow enhancements that I think
could start to address some of the use cases mentioned at the Galaxy
conference. This pull request
(https://bitbucket.org/galaxy/galaxy-central/pull-request/75/enhanced-batch-workflow-mode)
implements the backend for allowing multiple inputs to be selected on
multiple different params when running a workflow (currently Galaxy
only allows one input parameter to be batched). The UI piece has not
really been addressed but I was hoping to start a conversation on
that.

The backend currently has two processing "modes". I will illustrate
them with examples I heard about at the conference.

One thing I heard mentioned is batching processing paired FASTQ files
is difficult, and there were some hacks mentioned to address that. If
you pull in the above changeset, remove this line from run.mako:
$('.multiinput').addClass('disabled'); and ensure that this element is
set to "matched" in the form:



Then you can select multiple inputs on any number of parameters and
they will be matched up (based on the order they appear in the
history) and the workflow will be run for each match. Right know the
UI won't ensure that the same number of items is selected on each so
that piece should be added.

Someone else had mentioned doing sort of all versus all workflows (in
the context of microarray data). This is what I called product mode.
Again if you remove the JavaScript line mentioned above and ensure
that this element is set to product in the form:



Then you can select multiple inputs on any number of parameters and
the workflow will be run on each combination of the inputs.

To illustrate the difference - if user selected 5 inputs for one param
and 5 inputs for another in matched mode that will be run the workflow
5 times matching each input and in product mode it will run the
workflow 25 times with every combination of input pairs. If user
selects 6 inputs for one param and 4 for another, in product mode 24
workflows will run and in matched mode the submission will fail.

It should be straight forward to pull in the changeset and hack up
your Galaxy to do one or the other. I guess though we should allow
both and let the user decide :). I was hoping for some ideas on the UI
front, what the best way to communicate the differences, can we do
this without cluttering up the UI, should there be a separate advanced
workflow run mode, how do other workflow applications handle this
distinction, etc

One thought I had was allowing a choice between these two modes on a
per workflow basis is a nice step forward from where we are now, but
maybe another good step forward would be to allow the decision on a
per parameter basis. What I was thinking was maybe when you select the
little icon for multiple inputs, a broken link chain icon would appear
next to the multi-input icon indicating "product" mode would be
enabled for that input (i.e. the inputs are not linked), and then if
the user clicked the little broken chain on some parameters and those
chains would close (and maybe glow) and those parameters would become
"linked" (or matched).

Then you could mix and match, for instance you could run n*2 fastq
files paired off each against m different parameter files.

Mixing and matching would take a little more work, but if that makes
the UI more straight forward it might be worth it (I would be happy to
implement these extensions). Though I am pretty bad at UI so I assume
I am fairly off base on this link idea.

Thanks,
-John


John Chilton
Senior Software Developer
University of Minnesota Supercomputing Institute
Office: 612-625-0917
Cell: 612-226-9223
Bitbucket: https://bitbucket.org/jmchilton
Github: https://github.com/jmchilton
Web: http://jmchilton.net
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Re: [galaxy-dev] renaming fastq to fastqsanger

[Pete Schmitt]

The installation is mine.  It's using MySQL for the db.  I have two 
other installations.  This is the only one that holds the galaxy 
database directory on an nfs mount.  The other two installations don't 
exhibit this problem.  All 3 installations run on centos 5.8 using 
python 2.6.


Sent from my iPad

On Oct 5, 2012, at 3:24, Peter Cock > wrote:




On Wednesday, October 3, 2012, Pete Schmitt wrote:


When attempting the change the filetype of a fastq file to
fastqsanger, the process for changing the type goes on forever.  This
does not allow any further processing of the data.


That's strange - this should be really fast as it doesn't change the 
file on disk, just the metadata in Galaxy's database.


(The FASTQ groomer is much slower because it does write a new file)

Which Galaxy installation was this on? If yours, do you know anything 
about the setup (e.g. database used)?


Peter
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[galaxy-dev] Invitation to use Google Talk

[Google Talk]

---

You've been invited by suzan katie to use Google Talk.

If you already have a Google account, login to Gmail and accept this chat
invitation:
http://mail.google.com/mail/b-6dd94008a7-4956633c59-7YVOdLTCcdh4qfgxeie2tbh1sE4

To sign up for a Google account and get started with Google Talk, you can
visit:
http://mail.google.com/mail/a-6dd94008a7-4956633c59-7YVOdLTCcdh4qfgxeie2tbh1sE4?pc=en-rf---a

Learn more at:
http://www.google.com/intl/en/landing/accounts/


Thanks,
The Google Team
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[galaxy-dev] Crash on large workflow

[Todd Oakley]

Hello,
We have a rather large workflow (120 steps) that works on one of 
our Galaxy instances, but crashes Galaxy on another instance.  All the 
individual tools work on both instances. The error in paster.log is:


TimeoutError: QueuePool limit of size 5 overflow 10 reached, connection 
timed out, timeout 30


This is an older linux machine running CentOS, and there is no queuing 
system.



Is the queuepool limit a Galaxy variable? Or is this a limitation of how 
we have the machine configured?  I've tried searching the Galaxy wiki, 
but no luck yet.  I will keep searching, too.


Thanks!

Todd



--

***
Todd Oakley, Professor
Ecology Evolution and Marine Biology
University of California, Santa Barbara
Santa Barbara, CA 93106 USA
***

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Re: [galaxy-dev] Instant crash on large history export

[Jeremy Goecks]

Alex,

We'll need more details if we're going to figure out what the issue is. For 
example:

*are there certain dataset types that lead to a crash?
*what does the Galaxy log say (even if it's not interesting)?
*does the export job make it into the database and/or onto the cluster?

Any other info you can provide is appreciated.

Thanks,
J.

On Oct 5, 2012, at 10:08 AM, Bossers, Alex wrote:

> Another problem;
> On our ubuntu x64 server with the latest galaxy_central of Oct 4th...
> An export of the history sized 2.5Gb was ok. However large exports (like 
> 10Gb) make the server instantly crash (within a few seconds) without anything 
> significant in the galaxy.log.
> The apache server is still running though...
> 
> Help!
> Alex
> 
> 
> 
> 
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[galaxy-dev] Display data in browser

[Julian Pradinuk]

Hi,

I am proxying with Apache (and using xsendfile).

I wrote a wrapper for FastTree (http://www.microbesonline.org/fasttree/)
that uses the stderr_wrapper.py method to handle with stderr output.

When I click the display data in browser button (the eye) for the tree
output (txt file) I am prompted to download the file. It downloads as with
a file name and extension like 4HYYCqht.dms.part. Has anyone encountered
this issue before? Failing to see anything different in the apache logs..

Cheers,
Julian
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[galaxy-dev] "No module named controllers.library_common" error on fresh Galaxy install from 4-Oct-2012

[Anthonius deBoer]

I gave up on figuring out why jobs don't get started for 15 minutes and started a new instance of galaxy, but when I tried to create a new data library, I got this error...Error attempting to display contents of library (TEST DATA): No module named controllers.library_common.Any ideas?Thon
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Re: [galaxy-dev] "No module named controllers.library_common" error on fresh Galaxy install from 4-Oct-2012

[Scott McManus]

That's been fixed in a galaxy-central commit last night; the webapps were moved 
around, 
and this didn't point to the new webapps directory. See changeset 210c39f4bf7f 
or later. 
In particular, the problem you're seeing had to do with the 
templates/library/common/library_common.mako 
pointing to galaxy.web.controllers.library_common instead of 
galaxy.webapps.galaxy.controllers.library_common . 
A few other files had also been affected. 

-Scott 

- Original Message -




I gave up on figuring out why jobs don't get started for 15 minutes and started 
a new instance of galaxy, but when I tried to create a new data library, I got 
this error... 


Error attempting to display contents of library (TEST DATA): No module named 
controllers.library_common. 


Any ideas? 


Thon 
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[galaxy-dev] Galaxy October 5, 2012 Distribution & News Brief

[Jennifer Jackson]

*Galaxy October 5, 2012 Distribution & News Brief*
/http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05/

/*
Highlights:*
http://wiki.g2.bx.psu.edu/News

/

**

 *

   *BWA * tool wrappers /migrated
   
/
   to the *Galaxy Main Tool Shed *.

 *

   *Tool Factory* paper has been /E Published
   
/
   in PubMed  at *PMID: 23024011
   *.

 *

   The *Tool Shed Wiki * wiki
   has been re-written with a new, cleaner presentation. And check out
   all the /new features
   /!

 *

   Accessible *tool versions* in the UI and *new exit code features*
   enable /clearer experimental tracking and ease reproducibility
   /.

 *

   Release also includes *Visualization
   *
   updates, a new admin tool for /PostgreSQL
   / *Dataset cleanup
   *,
   and improvements in *API
   * , *Workflow
   *, and
   *Security
   *
   components.

http://getgalaxy.org
http://bitbucket.org/galaxy/galaxy-dist

*
new: * $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
*
upgrade:*   $ hg pull -u -r b5bda7a5c345

**

*
Thanks for using Galaxy!*

Jennifer Jackson & Galaxy Team

http://galaxyproject.org

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