Howdy All,
I was wondering if anyone has created a command line tool that will
add users to the Galaxy user database?
I did look into switching to external user authentication via nginx,
however, this will result in us using the campus wide kerberos system
and allowing ~30,000 people access to Ga
Peter,
Thank you so much for the help
> Date: Thu, 25 Apr 2013 18:35:33 +0100
> Subject: Re: [galaxy-dev] /bin/sh: 1: filename: not found
> From: p.j.a.c...@googlemail.com
> To: ramao_tiago_tibur...@hotmail.com
> CC: galaxy-dev@lists.bx.psu.edu
>
> On Thu, Apr 25, 2013 at 5:37 PM, Ramon Tiburski
Hi Dave:
Maybe some one knows a better way…
I would probably muck around in the database directly if there were a lot of
files.
One could probably move them all into a history, groom them, then pull the data
back into your libraries, deleting the old ones.
Brad
On Apr 25, 2013, at 4:58 AM, B
Hi Brad-
In the past, I had always been running the time-consuming fastqgroomer
step. However, based on this thread, I now realize this step is sometimes
unnecessary.
Here is my question. I have a large number of fastq data files that are
already in data libaries. They were imported in "fastq" fo
On Thu, Apr 25, 2013 at 5:37 PM, Ramon Tiburski
wrote:
> Hi Peter,
>
> I have this:
> filename $input $output
>
> And my executable and xml are in the same directory
>
> Thank you
If you don't put the binary on the system $PATH, then you'll
need to give an explicit path to it. You could try somet
Hi Peter,
I have this:
filename $input $output
And my executable and xml are in the same directory
Thank you
> Date: Thu, 25 Apr 2013 17:29:35 +0100
> Subject: Re: [galaxy-dev] /bin/sh: 1: filename: not found
> From: p.j.a.c...@googlemail.com
> To: ramao_tiago_tibur...@hotmail.com
> CC: galaxy-
On Thu, Apr 25, 2013 at 5:25 PM, Ramon Tiburski
wrote:
> I created a new tool in c++, and the "filename" is the name of my executable
> file. I have the xml and the executable file in the same directory, but I
> get this error when I try to run the tool. Someone can help me with this
> error?
>
>
I created a new tool in c++, and the "filename" is the name of my executable
file. I have the xml and the executable file in the same directory, but I get
this error when I try to run the tool. Someone can help me with this error?
Thank you
___
On Thu, Apr 25, 2013 at 4:25 PM, Dave Bouvier wrote:
> Peter,
>
> Your point is well taken about the utility of the testing framework in the
> tool development process. The framework has been modified as of
> 9520:41d8cdde4729 to only flag a changeset revision not to be tested if no
> valid tests
Peter,
Your point is well taken about the utility of the testing framework in
the tool development process. The framework has been modified as of
9520:41d8cdde4729 to only flag a changeset revision not to be tested if
no valid tests have been found in that revision. If one or more tools
have
On Thu, Apr 25, 2013 at 3:19 PM, John Chilton wrote:
> I agree that we shouldn't be hasty, but my two cents is that the
> galaxy-dev list should be split in two. Ironically, I think most of
> the traffic on this list right now is related to deployment issues -
> in that respect I would see it almo
On Fri, Apr 5, 2013 at 3:08 PM, Peter Cock wrote:
> On Thu, Apr 4, 2013 at 7:19 PM, Daniel Blankenberg wrote:
>> Hi Peter,
>>
>> What is the test error given when you do have a value defined for name in
>> output?
>>
>>
>> Can you try using 'empty_file.dat'?
>>
>> e.g.
>>
>>
>>
>> or
>>
I agree that we shouldn't be hasty, but my two cents is that the
galaxy-dev list should be split in two. Ironically, I think most of
the traffic on this list right now is related to deployment issues -
in that respect I would see it almost as Galaxy admins stay here and
developer chatter move to a
I was pretty much interested in Bio-Linux. However, the version of Galaxy that
comes with it is already outdated and there is no easy way to update it. It is
possible to delete it and re-install a newer version, this would be another
possibility...
Le 2013-04-25 à 05:50, Hans-Rudolf Hotz a écri
Hi Dave,
On Thu, Apr 25, 2013 at 2:27 PM, Dave Bouvier wrote:
> Peter,
>
> That is the intended behavior, but I've added a trello card
> (https://trello.com/c/O9YmzUT4) for revisiting that decision at some point.
Is that the right Trello card? Is seems to be all about multiple tool shed
reposito
Peter,
That is the intended behavior, but I've added a trello card
(https://trello.com/c/O9YmzUT4) for revisiting that decision at some
point. We are definitely willing to be flexible about the testing
conditions, but the primary goal of the automated testing framework was
to verify functiona
On Thu, Apr 25, 2013 at 1:40 PM, Dannon Baker wrote:
> Hey Peter,
>
> Thanks for the contributions, I've committed the changes to -central.
> You're definitely right about the merge failure not setting the job status
> to error, and I'm looking into that now.
>
> -Dannon
Thanks - that's likely to
Hi David
I have not used or tested it myself yet, but: have you looked into
"Bio-Linux" ?
The latest release (Bio-Linux 7) comes with Galaxy pre-installed, see:
http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-7-info
Regards, Hans-Rudolf
On 04/25/2013 12:52 AM, David Joly wrote:
Thanks
Hi Matthias,
you need to add something like the following to your tool defintion:
chemfp
The version and the name needs to be the same as in your
tool_dependency.xml.
Cheers,
Bjoern
> Björn,
>
> I have galaxy-dist. Was it the right choice?
>
> Here is what I did. I copied your "tool_de
Hey Peter,
Thanks for the contributions, I've committed the changes to -central.
You're definitely right about the merge failure not setting the job status
to error, and I'm looking into that now.
-Dannon
On Thu, Apr 25, 2013 at 6:51 AM, Peter Cock wrote:
> Hi all,
>
> While testing a BLAST s
On 04/24/2013 08:00 PM, Maddhi, Srinivas wrote:
> Third, should we start a separate email list for GalaxyAdmins
business? It would have far fewer members and have far less traffic
than Galaxy-Dev. I'm in favor of it. If you have an opinion, please
post here.
May want to wait until after we
Hi all,
While testing a BLAST search using plain text output (the 'txt'
datatype in Galaxy) or subclasses (like 'blastxml') using galaxy-dist
with task splitting enabled, I found I new bug when the files are
merged:
Error merging files global name 'shutil' is not defined
This is a side effect of
Hi dave:
The fastq groomer tool will convert your fastq files (of unknown base quality
scale) to fastqsanger. Are you sure these files are not already sanger scaled?
Modern illumina pipelines produce fastqsanger files.
If you do know the scale, just import the files explictly as fastqsanger (n
On Wed, Apr 24, 2013 at 10:12 AM, Peter Cock wrote:
>
> ..., I've still finding some other cases where despite having
> tests defined, nothing shows up on the Tool Shed test results page.
>
> Here's an example where I see that two tools (promoter2 and
> wolf_psort) have no tests, but the results o
On Wed, Apr 24, 2013 at 11:40 PM, Ganote, Carrie L wrote:
> Hi list,
>
> I have a newly installed Galaxy instance (security_2013.04.08) and I am
> testing out NCBI Blast+ on it. I'm having trouble getting it to run.
>
> I'm using the following tools from the Galaxy Main Toolshed:
> blast_datatypes
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