I'm running a local instance of Galaxy and have installed all the tool
dependencies and generated dependent files for Taxonomy Fetch.
After running the tool for like 20 minutes I get the following error.
*Dataset 43: Fetch taxonomic representation on data 37*
Tool execution generated the
thanks!
Hi,
I added your request to the card where we track these:
https://trello.com/c/mJWnAuuQ/1511-to-request-reference-genome-comment-on-this-card
Martin
Galaxy team
On Wed, Mar 26, 2014 at 3:17 PM, t...@caltech.edu wrote:
Hi Guys,
is it possible to add E.coli K12 genome for
Hi Jeremy,
I reverted the files that I have changed, and also cleaned the cache once
again. The error messages are the same:
Failed to load resource: the server responded with a status of 404 (Not Found)
require.js:1:1910Error: Script error for: libs/backbone/backbone-relational
Thanks!
I was able to side-step most of the fetch failures by copying the eggs by
hand into the eggs folder (copying them from an old galaxy-dist) or
installing them using pip. I have not applied the patch to test it, sorry.
I'll try it when I update.
My troubles started from trying to install
Hi Nate,
It's great to hear that my rearrangements for packaging Galaxy are
somewhat in line with what you are doing. My package is a bit of a
rats-nest of symlinks right now but I'll clean these up as things become
more configurable.
One thing I'm a bit stuck on is the tool_data_table_conf.xml
Hi Jeremy,
We found that the vis packed files were somehow not updated when we did the
Galaxy updates. So, we manually update these files and now the trackster is
working fine.
Thank you very much for the help!!
Best,
Shu-Yi
On Mar 29, 2014, at 7:51 PM, Jeremy Goecks wrote:
I cloned
Dear Galaxians,
I have galaxy running fine on a 8cpu machine, however I need to have it
submitting jobs to a linux cluster using PBS.
I got universe and job_conf.xml setup and as far as I use the local runner,
everything is fine.
However, whenever I try (e.g. clustalw) to use the DRMAAJobRunner,
On 31/03/2014 17:01, Luca Toldo wrote:
Dear Galaxians,
I have galaxy running fine on a 8cpu machine, however I need to have
it submitting jobs to a linux cluster using PBS.
I got universe and job_conf.xml setup and as far as I use the local
runner, everything is fine.
However, whenever I
In my case it was uncompleted metadata in one of the input files.
(but maybe it was not new state but something else?)
HTH,
ido
On Mar 26, 2014, at 5:25 PM, David Hoover hoove...@helix.nih.gov wrote:
I have many jobs stuck in the 'new' state on our local Galaxy instance. The
jobs can't be
I have opened a pull request that I believe could significantly ease
the operations like this (for instance grabbing a directory of similar
output files all of the same type based on a pattern specified by the
tool instead of by Galaxy). There are lots of details of in the pull
request body and
This turned out to be my own ignorance. After creating identical handlers in
both universe_wsgi.ini and job_conf.xml, and restarting Galaxy in daemon mode,
the jobs became resilient to Galaxy restarts. DOH!
Thanks Nate for pointing this out, as well as the limits collection.
David
On Mar
Happy April everyone!
It's a busy time in the
Galaxyhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_04 and
that is reflected in the April 2014 Galaxy
Updatehttps://wiki.galaxyproject.org/GalaxyUpdates/2014_04.
First, there were a record 63 new
Hi All --
I'm a novice when it comes to all things programming, but I recently
installed my own instance of Galaxy because I'm working with very large
datasets. Everything seems to be running OK, but when I attempt to run
Cuffdiff (w/ ref. annotation and bias correction from UCSC genome) on
Not sure if I've overlooked a setting somewhere, but is it possible to
customize or tweak the job descriptions that are displayed in the history?
Eg. Compute sequence length on data 1 isn't very descriptive, but if perhaps
the annotation field or a description field could be added it would make
Hi All,
We are getting errors when creating a workflow. Some of the tools,
when selected, say only error loading field data. As such, we cannot
use them in workflows, even though the tools work fine in Analyze Data.
This seems like it is correlated with the fact that we developed
Does anyone have a workable solution to managing and displaying large lists in
tool wrappers?
eg. a database list containing hundreds of enteries in the blast+ tool? (we
have 1,056 different blast databases).
As a work-around we've split our blast databases into species (eg cow, sheep,
fungus,
Hi Russell,
would something like a http://ivaynberg.github.io/select2/ field work
for you?
What do you mean with include tags? Are you aware of Galaxy macros?
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#Direct_XML_Macros
Cheers,
Bjoern
Am 31.03.2014 22:58, schrieb Smithies,
Greetings,
I am trying to add a new datatype in our Galaxy install to represent a TAR file
(we are trying to add a custom tool that produces a tarball of its output).
Is it possible to create a datatype of a TAR file (or ZIP, BZIP, GZIP, or any
other type of compressed file)? If so, what
Hi Bjoern,
Yes I'm aware of the macros but I've never managed to get them to work ;-(
What I'd like is something like a php include tag to pull the contents of a
whole file into another file so I'm not repeating myself eg. for the database
lists in the megablast, blastn, and tblastn wrappers.
Hi Russell,
Am 31.03.2014 23:46, schrieb Smithies, Russell:
Hi Bjoern,
Yes I'm aware of the macros but I've never managed to get them to work ;-(
Lets try to get them to work. It will do exactly what you want.
The Homer Tools should be a easy enough to get you started:
Those macros look great and are exactly what I want :-)
Thanx,
--Russell
-Original Message-
From: Björn Grüning [mailto:bjoern.gruen...@gmail.com]
Sent: Tuesday, 1 April 2014 11:07 a.m.
To: Smithies, Russell; Björn Grüning; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Managing
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