On Wed, Jun 8, 2011 at 9:59 PM, Jim Johnson wrote:
>
> It went into galaxy-central:
>
> $ hg log -pr 5082
> changeset: 5082:a86e1fa82a89
> user: Kanwei Li
> date: Thu Feb 17 15:35:07 2011 -0500
> summary: Add a "format_source" attribute to the ToolConfig output data
> element
Hi,
Is it possible to tell Galaxy to use the bare username passed back by
external authentication as the email address without appending any
domain? It seems to complain if it isn't in email address format and
asks you to set up a domain to append in universe.wsgi.
I would like to use the bare u
Hello everybody,
currently I have some trouble with the following kind of error:
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position
155: ordinal not in range(128)
We have encountered it twice now. The first time it was related to a
shared library, which could not be opened
Hi all,
I just updated our development machine to the latest from galaxy-central,
and it broke:
$ ./run.sh
Traceback (most recent call last):
File "/home/pjcock/repositories/galaxy-central/lib/galaxy/web/buildapp.py",
line 81, in app_factory
from galaxy.app import UniverseApplication
File
Hi again,
Sorry to ping again about this, just very interested in knowing if
this is a missing feature in Galaxy or if I had configured something
wrong.
Is it possible in Galaxy to have a tool with a multiple="true" input
dataset parameter? It doesn't seem so?
best,
Leandro
On Tue, May 24, 20
Also want to ping again about this possible bug or feature.
-Leandro
On Fri, May 13, 2011 at 2:57 PM, Leandro Hermida
wrote:
> Hi all,
>
> In a tool XML I have a select menu param within/driving a conditional tag
> and in the workflow editor it doesn't let me choose to allow the user to set
> th
> On Fri, May 13, 2011 at 2:57 PM, Leandro Hermida
> wrote:
>> Hi all,
>>
>> In a tool XML I have a select menu param within/driving a conditional tag
>> and in the workflow editor it doesn't let me choose to allow the user to set
>> this select menu at runtime? Is this a bug?
>>
>> best,
>> lean
Hi,
I am new to galaxy, I just downloaded and installed galaxy on my MAC system. I
also download bowtie , and it is working perfectly on the command line. But am
not able to see the bowtie option under mapping in the galaxy menu. Do I have
to do another modifications like move into particular f
On 06/09/2011 02:47 PM, Arun Selvam wrote:
Hi,
I am new to galaxy, I just downloaded and installed galaxy on my MAC
> system. I also download bowtie , and it is working perfectly on the
> command line. But am not able to see the bowtie option under mapping
> in the galaxy menu.
Are you sure,
I added an example taken from trim.seqs.xml in the Mothur metagenomics
tool_suite to:
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax
The following will create datasets in the history panel, setting the output data type to
be the same as that of an input dataset named by
On Tue, May 17, 2011 at 2:21 PM, Nate Coraor wrote:
> Peter Cock wrote:
>>
>> That sounds really useful - it is something that you plan on adding
>> to Galaxy officially?
>
> Yes, I'm working on adding a lot of user- and admin- side access to
> various numbers about disk usage (used by histories,
On Thu, Jun 9, 2011 at 11:43 AM, Peter Cock wrote:
> Hi all,
>
> I just updated our development machine to the latest from galaxy-central,
> and it broke:
>
> $ ./run.sh
> Traceback (most recent call last):
> File "/home/pjcock/repositories/galaxy-central/lib/galaxy/web/buildapp.py",
> line 81, i
Hello Peter,
On Jun 6, 2011, at 6:41 AM, Peter Cock wrote:
> On Thu, Jun 2, 2011 at 6:39 PM, Greg Von Kuster wrote:
>>
>> We will certainly include support for new data formats into the Galaxy core.
>> In case you haven't seen it, details for adding new formats is available in
>> our wiki at h
Peter Cock wrote:
>
> It turned out to be quite quick to find what commit broke things:
>
> hg checkout 6074:a6868407f0e8
> --> fails
>
> hg checkout 6073:d6b048e3483e
> --> works
>
> Looks like 6074:a6868407f0e8 is the cause then, which makes sense
> since it jumps from NumPy 1.3.0 to NumPy 1.
Hi and thanks to you both !
Jim : I tryed your solution and it works just fine !
Peter : thanks for the advice, I'll support only sff/fastq as inputs
you're right it makes think easier !
Jerome
Peter Cock a écrit :
On Wed, Jun 8, 2011 at 4:36 PM, Mariette wrote:
Hi everyone,
I'm fac
Peter Cock wrote:
> On Tue, May 17, 2011 at 2:21 PM, Nate Coraor wrote:
> > Peter Cock wrote:
> >>
> >> That sounds really useful - it is something that you plan on adding
> >> to Galaxy officially?
> >
> > Yes, I'm working on adding a lot of user- and admin- side access to
> > various numbers abo
Fixed on trunk.
On Thu, Jun 9, 2011 at 10:26 AM, Nate Coraor wrote:
> Peter Cock wrote:
> >
> > It turned out to be quite quick to find what commit broke things:
> >
> > hg checkout 6074:a6868407f0e8
> > --> fails
> >
> > hg checkout 6073:d6b048e3483e
> > --> works
> >
> > Looks like 6074:a68684
On Thu, Jun 9, 2011 at 3:17 PM, Greg Von Kuster wrote:
> Hello Peter,
>
> On Jun 6, 2011, at 6:41 AM, Peter Cock wrote:
>
>> On Thu, Jun 2, 2011 at 6:39 PM, Greg Von Kuster wrote:
>>>
>>> We will certainly include support for new data formats into the Galaxy core.
>>> In case you haven't seen it
On Thu, Jun 9, 2011 at 4:25 PM, Kanwei Li wrote:
> Fixed on trunk.
Confirmed, thank you.
Peter
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On Thu, Jun 9, 2011 at 8:39 AM, Peter Cock wrote:
>
> Thanks for this, I can think of several of my own tools where this
> will work much more cleanly than the current solution using
> and .
>
There is still a bit of work needed:
https://bitbucket.org/galaxy/galaxy-central/issue/582
#582 output
Hey Greg,
Unfortunately after pulling your changeset I got a new error related to
'1_field_name'. Here is the error traceback:
URL:
http://localhost:8080/requests_common/add_samples?cntrller=requests&id=f2db41e1fa331b3e
File
'/home/jcruz/galaxy-central/eggs/WebError-0.8a-py2.6.egg/weberror/eva
Chorny, Ilya wrote:
> I am trying to figure out how to pass the current user name to drama.py. I
> have had little success so far. None of the environmental variables contain
> any current user information. Any thoughts?
>
> Thanks,
>
> Ilya
Hi Ilya,
You can use $__user_email__ in the command
Leandro Hermida wrote:
> Hi,
>
> Is it possible to tell Galaxy to use the bare username passed back by
> external authentication as the email address without appending any
> domain? It seems to complain if it isn't in email address format and
> asks you to set up a domain to append in universe.ws
John,
Questions about local installs are best directed to galaxy-dev, so I've moved
the question to this list.
>> While executing cuffcompare, I encountered this error message:
>>
>> Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output'
>>
>> I was practicing RNA-seq anal
Hi,
with the new ToolShed inplace, and support for cloning/pulling tools directly:
What's the recommend way to organize the repositories ?
For example, I want to use Peter's Venn tool:
hg clone http://toolshed.g2.bx.psu.edu/repos/peterjc/venn_list
If I clone, I get the following folder hierarchy
On Thu, Jun 9, 2011 at 7:15 PM, Assaf Gordon wrote:
> Hi,
>
> with the new ToolShed inplace, and support for cloning/pulling tools
> directly: What's the recommend way to organize the repositories ?
>
> For example, I want to use Peter's Venn tool:
> hg clone http://toolshed.g2.bx.psu.edu/repos/pe
Hi Peter,
On Jun 9, 2011, at 12:02 PM, Peter Cock wrote:
>>
>
> Is there anything documented about the built-in format conversion
> within the Galaxy core, rather than tools.
No, not currently - except for a few details in various slide presentations.
Nothing forma though. We're trying to
In addition to cloning, you can also download the tarball for each tool just
like you used to - see the Repository Options popup menu for each repo.
On Jun 9, 2011, at 2:55 PM, Peter Cock wrote:
> On Thu, Jun 9, 2011 at 7:15 PM, Assaf Gordon wrote:
>> Hi,
>>
>> with the new ToolShed inplace,
Hi Nate,
Thank so much for the instructions :) , yes this is what I would want
to do as Galaxy was adding an empty @ after the username. Yep in a
Windows domain environment the bare username (sAMAccountName) is also
an email nickname and works with the Exchange server when you use SMTP
services.
Joe,
Try editing your Sample Form Definition, changing the "Field name" value from
the default of "1_field_name" to be your desired "agctac". Then, your csv file
with the line
Sample1,Library1,Lib1Folder1,History,Workflow,agctac
should work.
Greg
On Jun 9, 2011, at 6:03 PM, Joe Cruz wrote:
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