Hi Devs,
I'd like to open up some discussion about incorporating some code bits into the
Galaxy distribution.
My code is here:
https://bitbucket.org/cganote/osg-blast-galaxy
First off, I'd like to say that these changes were made initially as hacks to
get Galaxy working with a grid interface
Hi List,
I am wrapping a Galaxy tool for the GFFread utility from Cufflinks. It has a
few optional files as inputs, but I can't get this to translate to the tool
wrapper.
I started with a tool that has an advanced options menu. When this is selected
as advanced, it brings up a bunch of
Hi List,
I've noticed that the mechanisms for catching job termination signals don't
seem to apply to uploading jobs. I was having trouble with *any* jobs being
terminated until I pulled Nate's changeset 1298d3f from Galaxy central, but it
still doesn't work for uploads. It will remove them
, any other sleuthing suggestions would be greatly
appreciated.
Sincerely,
Carrie Ganote
From: Hans-Rudolf Hotz [h...@fmi.ch]
Sent: Wednesday, March 12, 2014 5:07 AM
To: Ganote, Carrie L
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] History
Hi List,
I just pulled and merged from galaxy-dist (I think it's dc067a95261d), updated
my database, and migrated my tools. The issues I am able to see are minor, but
I have a user who can no longer access a particular history. It apparently just
hangs. If they delete the history, Galaxy
I just pull 6dc and replace the files I need
from bf3 manually?
Thanks so much for the advice,
Carrie Ganote
From: Nate Coraor [n...@bx.psu.edu]
Sent: Thursday, February 27, 2014 8:49 AM
To: Ganote, Carrie L
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev
Hi Galaxy devs,
I had an issue recently where I must have messed up my .hgignore file or done
something terrible to my repository.
I created a bitbucket and pushed my instance to it. I then pulled that onto my
laptop and hooked it all up with Eclipse. After I was happy with my code, I
pushed
Hi List,
It seems that the blastdb and blastdbp data format is not respected on my local
install; is it just not generally defined, or am I missing something in
/lib/galaxy/datatypes or in datatypes_conf?
The most recent blasp wrapper includes this for the input parameter:
type=data
: Peter Cock [p.j.a.c...@googlemail.com]
Sent: Wednesday, October 30, 2013 5:59 PM
To: Ganote, Carrie L
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: Blastdb and blastdbp datatypes not enforced
On Wed, Oct 30, 2013 at 9:22 PM, Ganote, Carrie L cgan...@iu.edu wrote:
Hi List,
It seems
Hi List,
I've sprouted some grays in the last week after my Galaxy instances all
simultaneously ceased to submit jobs to our main cluster.
Some Galaxy instances are running the PBS job runner, and others use DRMAA. For
the DRMAA runner I was getting:
galaxy.jobs.runners ERROR 2013-10-15
Hi List,
I'm a bit baffled by a new tool I've tried to add to Galaxy. The job runner
does not dispatch it correctly.
I added the tool via the toolshed, set up the executable on the cluster side,
and attempted to hook it up to the dynamic job runner. The destination always
ended up set as
saved me a re-install and quite a bit
of sanity.
Sincerely,
Carrie Ganote
From: jmchil...@gmail.com [jmchil...@gmail.com] on behalf of John Chilton
[chil...@msi.umn.edu]
Sent: Monday, October 07, 2013 2:02 PM
To: Ganote, Carrie L
Cc: galaxy-dev
Hi List,
I've run into a frustration recently with passing values to the dynamic job
runner from a tool. Here's what's going on:
in ncbi_blastn_wrapper.xml:
param name=pathToModule type=hidden value=/abs/path/to/module /
...
in dynamic_runner.py:
...
def blastn_wrapper(job):
incoming =
...@msi.umn.edu]
Sent: Wednesday, August 07, 2013 3:52 PM
To: Ganote, Carrie L
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Tool params passed to python dynamic job runner
I am not sure why the quotations marks are there in the first place,
but I do see the problem. replace and strip
Hi list,
I ran into the following problem:
$ sh run_galaxy_listener.sh
Traceback (most recent call last):
File scripts/galaxy_messaging/server/amqp_consumer.py, line 33, in module
from galaxy.web.api.requests import RequestsAPIController
ImportError: No module named api.requests
Changed
Hi folks,
First of all, I really love the new job configuration style. It makes it very
easy to change swaths of jobs and to streamline the way jobs are submitted to
the cluster. I had no issues with the dynamic runner and I like the way that
tags interact. My question is for the dynamic job
Hi Peter,
How did you install them? Via the automated Tool Shed install,
or manually?
I installed the tool wrappers via the Tool Shed, and Blast 2.2.28 is already
installed on my cluster so I put the path in my environment setup file.
How did you setup the databases?
I added the existing
Hi Peter,
I'm not 100% sure but I think the BLAST 2.2.26+ which Galaxy installed
via the Tool Shed will take priority over the system installed BLAST 2.2.28+
already on the cluster.
Blast 2.2.26 probably would take priority, if I installed it =D but I didn't
set up the missing tool
Hi list,
I installed the latest toolshed NCBI Blast+ into a new Galaxy and I'm trying to
pinpoint these errors:
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other
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 b3a3ba0c1d47
ncbi_blast_plus 1f546099212f
Looks like blast is being
Of Ganote, Carrie L
Sent: Friday, 5 April 2013 4:52 AM
To: galaxy-...@bx.psu.edu
Subject: [galaxy-dev] PBS_Python Unable to submit jobs
Hi Galaxy dev,
My setup is a bit non-standard, but I'm getting the following error:
galaxy.jobs.runners.pbs WARNING 2013-04-04 13:24:00,590 (75) pbs_submit failed
(try
Hi Galaxy dev,
My setup is a bit non-standard, but I'm getting the following error:
galaxy.jobs.runners.pbs WARNING 2013-04-04 13:24:00,590 (75) pbs_submit failed
(try 1/5), PBS error 15044: Resources temporarily unavailable
Here is my setup:
Torque3 is installed in /usr/local/bin and I can use
Hi Galaxy-Dev,
I have a new local instance that submits to cluster1 via pbs-drmaa-1.0.14.
Galaxy is on a VM that is a submit node on cluster1, and there is a shared
filesystem amongst all the clusters where the datasets are stored. The Galaxy
VM is also a submit node on cluster2 and we have
Hi all,
I am trying to upgrade our instance to the newest dist but I get the following
in stderr when I attempt to run Bowtie or BWA:
PREFIX/subs/galaxy_31.sh: command substitution: line 7: syntax error near
unexpected token `('
PREFIX/subs/galaxy_31.sh: command substitution: line 7: `diff -n
: Wednesday, March 27, 2013 1:56 PM
To: Ganote, Carrie L
Cc: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Tool run on cluster returns error state on clean
install
Hello Carrie,
Ganote, Carrie L wrote, On 03/27/2013 01:22 PM:
I am trying to upgrade our instance to the newest dist but I get
[ja...@jamestaylor.org]
Sent: Friday, January 04, 2013 2:45 PM
To: Ganote, Carrie L
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Viewing Galaxy in Ipad
The fix is in this changeset, applied conditionally on iOS devices:
https://bitbucket.org/galaxy/galaxy-central/commits
Hi all,
Right now I have drmaa running with Torque. I have a virtual machine with
Galaxy installed on it, a filesystem mounted on the virtual machine that holds
the dataset info, and a cluster that runs big jobs and also has access to the
mounted filesystem. When running Galaxy as a real
Hi Alex,
I see what you are saying, but I think our situations are slightly different.
The line
self.__user_system_pwent =
pwd.getpwnam(job.user.email.split('@')[0] )
*does* return the correct username, however, that user is not present in the
Virtual machine that is running
Hi all,
I could use some help getting DMRAA to run. We already have a galaxy instance
with pbs running, but I'd like to connect to Torque using dmraa because we
eventually intend to port over to a different resource manager.
I've followed these instructions:
Hi all,
I've browsed a few of the public Galaxies to get an idea of what I like and
don't like; I've noticed that some of the instances have an accordion
behavior where when one of the tool sections is expanded, all others collapse.
In galaxy main, you can have multiple tool sections open at
Hi all,
I'm trying to make a tool that takes, as input, a dataset of type=data and
format = axt,fasta. I want to run the axt_to_fasta tool if the input is axt
and the fasta_to_tabular if the input is fasta.
Basically, I want to wrap all the type conversions into one tool, since it
seems like
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