Hello,
I'm new to Galaxy so I think i'm at the right place asking this, though
please let me know if I got it all wrong.
I sent a Tophat query on Thursday about 5 days ago and it is still waiting
to ran (gray background).
Is to O.k? A bug? Should i keep waiting or stop everything and restart?
On Tue, Apr 30, 2013 at 3:56 AM, Mike Dyall-Smith
mike.dyallsm...@gmail.com wrote:
This follows on from Kenneth Auerbach's question Sep 12, 2012: Galaxy error
running NCBI BLAST: blastx
http://dev.list.galaxyproject.org/Galaxy-error-running-NCBI-BLAST-blastx-td4656210.html
I wish to use a
On Wed, Apr 24, 2013 at 6:02 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hello all,
I can't be the only Galaxy Tool author to have accidentally
made a change on the main Tool Shed my mistake, wrongly
assuming I was on the test Tool Shed (sandbox). In this case
the tool update was
Dear dev,
I have two questions
1) Is there a function that I can use to delete a dataset from the history?
I have a tool that uses as input a hidden dataset and I want to delete
the hidden dataset once the tool is executed.
I have the filename of the dataset and I was wondering if there is a
I have been trying to join the intervals of two datasets side-by-side using the
public Main instance, but the job never finishes. I've gotten a message stating
that Galaxy is unavailable a couple of times, but I have tried running this job
multiple times with no success. I also tried to upload
Peter,
That was my mistake, I had put that on my todo list, but neglected to
make a trello card. Thank you for the reminder, I've moved the card to
the appropriate section.
--Dave B.
On 4/30/13 06:38:26.000, Peter Cock wrote:
On Wed, Apr 24, 2013 at 6:02 PM, Peter Cock
I have been trying to join the intervals of two datasets side-by-side, but the
job never finishes. I've gotten a message stating that Galaxy is unavailable a
couple of times, but I have tried running this job multiple times with no
success. Any help will be greatly appreciated.
Thanks,
Hello,
I am a student, and I am using the psu galaxy server for an assignment. My
workflow for each of my 5 data sets has been waiting to run 3 jobs (bwa
alignment, sam to bam, and bam statistics). One of my datasets reached
completion two days ago, but it has been 5 days for the others.
Dear dev
I would be grateful for some assistance in setting up our galaxy server to
submit jobs to our torque server.. We are using release_2013.04.01
I have tried going through the install information but clearly I’ve
misunderstood something, and unfortunately most examples come from
[Apologies for my previous email : finger slippage meant I sent before
completing the email]
Dear dev
I would be grateful for some assistance in setting up our galaxy server to
submit jobs to our torque server.. We are using release_2013.04.01
I have tried going through the install
On Thu, Apr 25, 2013 at 3:36 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
OK, I've updated to the latest galaxy-central default branch. Here's
the slightly revised test for ncbi_makeblastdb.xml,
...
In the absence of any fresh feedback, I've filed an issue on Trello for this
to make sure
On Mon, Apr 29, 2013 at 3:30 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Dave,
What was the relevant Trello card, and does it cover other
limitations like how to use repeat parameters in a test case?
Thanks,
Peter
I've filed a Trello issue for the specific problem with conditional
Hi David,
These short courses may be of interest:
http://scriptogr.am/ohofmann/intro-to-galaxy
http://scriptogr.am/ohofmann/rna-seq
http://scriptogr.am/ohofmann/exome-seq
Ilya
On 4/25/13 10:11 AM, David Joly idj...@gmail.com wrote:
I was pretty much interested in Bio-Linux. However, the
Hello all,
Given the precedent that the test framework uses tool_conf.xml.sample
rather than tool_conf.xml, I would expect it to use example.loc.sample
rather than example.loc when running unit tests with parameters whose
values come from a loc file. This is not the case.
When writing unit tests
Hi All,
I am trying to get Freebayes installed on a cloud man instance from the galaxy
toolshed. I have successfully installed the Samtools 0.1.18 package, but the
freebayes package errors.
The Error is:
Tool shed repository: freebayes
Tool shed repository changeset revision: 28e422c589ac
Looks like you're missing cmake, a dependency for building FreeBayes. If
you're able to install that for your system (available in most package
managers) you should be good to go.
-Dannon
On Tue, Apr 30, 2013 at 1:03 PM, Iry Witham iry.wit...@jax.org wrote:
Hi All,
I am trying to get
Lilach,
Is this on your own install of Galaxy or the public ones? If its on
the public ones offered by the Galaxy community, I think you need to
post to the users list. If its own your own custom install of Galaxy,
you need to check that the job runners have been configured correctly.
-Adam
--
Hi everyone,
Is there an easy way to view/save/print out the executed commands and their
parameters for a workflow? I want to see what is going on for certain steps
in my workflow.
Regards,
Hak
___
Please keep all replies on the list
Hi Hak,
Yes, you can get all of the information saved for a particular workflow -
in the abstract, not a particular workflow execution - by going to
'Download or Export' in the workflow menu, then click Download to File.
This will give you a .ga file which contains the steps in JSON format,
You'll want the job table, and the field is command_line.
On Tue, Apr 30, 2013 at 3:26 PM, Hakeem Almabrazi halmabr...@idtdna.comwrote:
Yes, I am actually looking for the actual command lines that were
executed. I would like to know exactly how these tools are called so I can
mimic that
Hi,
I have some tools that run really quickly without using any kind of cluster.
I would prefer not to run these tools on a cluster, as the overhead of
submitting these jobs makes them take much longer than they otherwise
would.
I have other tools that are computationally intensive and need to be
Hey Dan,
Sure, you can configure per-tool job runners. This wiki page (
http://wiki.galaxyproject.org/Admin/Config/Jobs) should get you started,
but let me know if you run into any troubl
On Tue, Apr 30, 2013 at 4:47 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Hi,
I have some tools that
1) Any idea which proxy settings in the universe_wsgi file need to be set
other than the ones on the website? Those are the only ones I changed. I
scrolled down to the 'Advanced Proxy' settings but didn't see anything that
looked relevant to me.
Probably I should have sent this earlier, but
Thank You Danno,
I will give it a try. By the way, is there a way to run a workflow and create
a new history every time new data sets (fastq) is available programmatically?
I have looked at the scripts at the ~api/ (ie. Example_watch, workflow_excute)
scripts but I do not think these scripts
Yep, you can do this. In example_watch_folder.py, ~line 65, notice that
the payload for the workflow post includes a 'history' key, which is the
name of newly created history. In this particular example, it just names
it Dataset Name - Workflow Name, but you could use anything there.
On Tue,
Hey Rob,
I haven't touched in quite some time, but from the comments it indicates
that the sleep was because the datatype hadn't been detected and set yet,
so that's what I'd check for -- specifically result_ds['data_type'] being
something sensible (I have no idea what it is by default off the
Dear Dev Team,
My program that I'm trying to integrate with Galaxy relies on SQLite
databases to hold gene annotation information throughout multiple stages
of processing. Given that the .db files produced by SQLite are not one
of the standard data file types, is there any provision for a
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