Hi Tobias,
Maybe your Galaxy is running in daemon mode. If that is the case, if you do 'ps
aux | grep universe' you will see something like:
python ./scripts/paster.py serve universe_wsgi.ini --daemon
You should first stop the daemon. Or you kill it, or you type in the galaxy
home './run.sh stop
Hi,
First make sure that the you are editing the correct universe_wsgi.ini
file. Secondly, you must restart your server after you make changes to your
settings file i.e universe_wsgi.ini. If you are running your server
in daemon mode use following command to stop your server:
*sh run.sh --stop-dae
Hello,
When I run tophat ("Tophat for Illumina Find splice junctions using
RNA-seq data ), the job failed with truncated files. However, index
files are available and I get exactly the same error message using
built-in index or one of my history.
/
Tool execution generated the following err
Hi ,
when I use: sh run.sh --stop-daemon
to start the server, I get:
No PID file exists in paster.pid
when I use : ps aux | grep universe
I get: tobikenobi 3013 0,0 0,0 2435548 0 s000 R+9:25pm 0:00.00
grep universe
- Original Message -
>> From: Sachit Adhikari
>> To: Ma
Hi,I need to create a new tool in c++, but I'm with a lot of difficult to link
the cpp or exe (I don't know) with the xml document. Can you help me with an
example that receives a txt file with a phrase and shows another txt file
without the spaces of this phrase?
Thanks
I have not seen any reply to this question from last year, so I wanted to re-up it again...I also run into this issue quite often and with the recent introduction of the (half completed?) feature of the notion of Paused-Jobs it seems we are getting very close to this working...I know I can re-run a
Related, but not automatic retries in case of node failures -- you can
follow the progress of workflow continuation (without rerunning, etc) here:
https://trello.com/c/kpARiWl5
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in y
I started studying the galaxy and would like to know about the power of this
tool, you could tell me why using the galaxy and what are its advantages
compared to other similar systems. And another question, can I adapt galaxy to
another area like the agronomy, only with creating new tools?
Thank
I noticed that the latest versions for Bowtie2 and Tophat2 listed on the
Tool Dependencies page
(http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies) are
2.0.4 for Bowtie2 and 2.0.6 for Tophat2. Are these the latest supported
versions? Does anyone know if it's advisable to go with t
We are using bowtie 2.1.0 in via a galaxy wrapper. Since there has been no
change in the bowtie command line options used by the wrapper, there are no
problems.
Similar for Tophat.
Brad
On Apr 10, 2013, at 3:05 PM, Lance Parsons
wrote:
> I noticed that the latest versions for Bowtie2 and Top
Hi,
I am not an expert in all Galaxy capacities. We have been built some new
tools in Galaxy platform:
1. Evolutionary Algorithms for Protein Structure Prediction.
2. Protein Validation
3. Protein desolvate
You can find more information about them at [1]. These tools are beta
version ye
Hello all,
First, thanks to Srinivas and Hans for the responses.
I have kept track of the head counts for most meetups:
2012/07/07 27
2012/07/27 ? (in person meetup at GCC2012)
2012/09/19 10
2012/11/07 17
2013/01/16 14
2013/03/20 15
So, maybe converging on mid-teens? This number is not
Hi Sarah,
Let's try to sort this out. Your problem does not seem to be the same as
in the question referenced, but we can see. First - just to double check
- since setting up the genome, you have restarted the server? If not, do
that first and check to see if that fixes the problem. Basically,
Dear all, I am trying to follow the Admin Add Tool Tutorial [1]. I put my
binary BINARY into the location ${galaxy_root}/tools/${category}/BINARY.
However, it is not found using if the tag looks as follows:
BINARY (arguments)
When I put the following, it works:
$__root_dir__/tools/CATEGORY/BI
Hi Manuel,
is your XML file also under ${galaxy_root}/tools/${category}/ ? It
should be.
Tata,
Bjoern
> Dear all, I am trying to follow the Admin Add Tool Tutorial [1]. I put my
> binary BINARY into the location ${galaxy_root}/tools/${category}/BINARY.
> However, it is not found using if the
Yes, this is the case.
I have:
galaxy-dist/tools/${category}/BINARY
galaxy-dist/tools/${category}/BINARY.xml
Where BINARY.xml contains the BINARY... XML code.
Is there a good way to see what Galaxy is exactly executing for the tool? I
could not find a description on how to do that anywhere on
Hi Ramon,
> Hi,
> I need to create a new tool in c++, but I'm with a lot of difficult to
> link the cpp or exe (I don't know) with the xml document. Can you help
> me with an example that receives a txt file with a phrase and shows
> another txt file without the spaces of this phrase?
Your c++ bin
If I want to add a new datatype during tool installation from the shed, how
define that in the tool.xml? Is this documented anywhere?
-Robert
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Hey Robert,
Yep, it's documented here:
http://wiki.galaxyproject.org/ToolShedDatatypesFeatures
-Dannon
On Wed, Apr 10, 2013 at 5:50 PM, Robert Baertsch wrote:
> If I want to add a new datatype during tool installation from the shed,
> how define that in the tool.xml? Is this documented anywher
Hi,
> I have:
>
> galaxy-dist/tools/${category}/BINARY
> galaxy-dist/tools/${category}/BINARY.xml
Try to put the binary in your PATH.
> Where BINARY.xml contains the BINARY... XML code.
>
> Is there a good way to see what Galaxy is exactly executing for the tool?
In your webX.log. It is depe
Hi Robert,
> If I want to add a new datatype during tool installation from the
> shed, how define that in the tool.xml? Is this documented anywhere?
> -Robert
See here:
http://wiki.galaxyproject.org/ToolShedDatatypesFeatures
Regards,
Bjoern
>
Adding galaxy-dist/tools/${category} to PATH before calling sh run.sh does the
trick. This is not ideal but works for now...
Thanks,
Manuel
From: Björn Grüning [bjoern.gruen...@pharmazie.uni-freiburg.de]
Sent: Thursday, April 11, 2013 12:19 AM
To: Holtgrew
Dear all,
is it possible to make Galaxy use a specific extension for a given data type
without a wrapper?
I.e. can I make Galaxy use the extension .bam, .sam, .fasta etc. internally
instead of .dat?
Thanks,
Manuel
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