e will have some idea from the
subject line if they should read it or not.
2. Not doing this greatly increases the number of emails that match search
queries, but that aren't actually informative.
Today's Topics:
1. pbs_python issues (Iry Witham)
2. Which css file does welcome.html
OK, this is ostensibly a simple question. However, I can't find the CSS file
that welcome.html is using. In the HTML file, there's this line:
However, I don't see a directory named "style" anywhere in the galaxy directory
tree. When I search for "base.css," from the root Galaxy installation
d
We have an instance of Galaxy deployed on a local institutional cluster. It's
working well, but when we import BED files for visualization, Galaxy runs the
processing for these on the cluster. I would like to run these tasks locally
instead.
I understand how to make individual tools run locally
Good catch, thanks Nate! I have plenty of tool_runners defined, but no
tool_handlers. Do I have to specifically assign tool handlers in order for them
to be used in job deployment?
Thanks!
Dan
>Hi Daniel,
This parameter should be 'job_handlers'
Are there any entries in your [galaxy:tool_han
I have galaxy running on my institution's cluster computing service, which uses
PBS. It's in a balanced configuration.
Jobs going to the cluster submit without any problem at all. However, any job
that I have specified to run locally in the universe_wgsi.ini file won't
dispatch. There isn't any
Thanks Nate! That's very helpful.
-Original Message-
From: Nate Coraor [mailto:n...@bx.psu.edu]
Sent: Friday, June 08, 2012 3:31 PM
To: Dorset, Daniel C
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] How does Galaxy access datasets?
On Jun 5, 2012, at 6:08 PM, Dorset, D
I appreciate you taking the time to help! I'm almost positive it's a local
configuration issue, like you said, but without knowing how Galaxy generates or
parses its internal links (in the form of [Galaxy web address]/datasets/[16
character hash]/display/[filename] ) it's tough to know how to at
Dan
-Original Message-
From: Ross [mailto:ross.laza...@gmail.com]
Sent: Wednesday, June 06, 2012 6:07 PM
To: Dorset, Daniel C
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] I can't see or access pictures in FastQC
Hi, Daniel.
The wrapper doesn't introduce any new dep
I'm running two separate instances of Galaxy on two different servers. On both
servers, whenever I run FastQC, I can see the result HTML file, but none of the
pictures show up. Furthermore, if I try to access the links at the bottom of
the page, they don't lead to any real files.
If I look in m
I'm trying to troubleshoot why I can't retrieve output from my Galaxy cluster
instance. I notice that when I click on any output, the URL is something like:
http://[root galaxy address]/datasets/[some 16-character hash]/display/[file
name]
I'm not able to find the "datasets" directory on the lo
Thanks Nate! I'm looking forward to it!
-Original Message-
From: Nate Coraor [mailto:n...@bx.psu.edu]
Sent: Thursday, May 10, 2012 11:02 AM
To: Dorset, Daniel C
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Running Galaxy on PBS/Torque cluster
On May 3, 2012, at 3:
Hi Mish,
In the proftpd.conf file, do you have the "user" and "group" fields set to your
Galaxy user and group?
Let me know if the question needs further clarification.
Thanks,
Dan
Message: 10
Date: Wed, 9 May 2012 08:21:19 +
From: Misharl mon
To:
Subject: [galaxy-dev] FTP Problem: User
I have had Galaxy running on a local BAS, and after success with that we're
ready to create an instance on our local cluster computing service. The local
cluster uses PBS/Torque.
I'm familiar with the basics of configuration, but our particular scheduler
rewards those who specify accurate wallt
Hi Ann,
Count me in. Great idea!
-Dan
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Fantastic! Knowing that it's not coming from Galaxy is very helpful.
Thanks again,
Dan
-Original Message-
From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
Sent: Thursday, April 19, 2012 1:56 PM
To: Dorset, Daniel C
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: How to specif
Thanks Jeremy, that's very helpful, and it's great to hear from a developer!
I have been pursuing option (a), and I feel like I'm very close. The RUM tool
runs, and the filesizes show up in the history, but the datasets show up as
erroneous. When I click on the apparently-problematic dataset's b
I'm currently writing a Galaxy wrapper for RUM (RNA-seq Unified Mapper). RUM is
a tool that generates many output files. It is run from the command line using
the following syntax:
RUM_runner.pl
[options]
I'm good with everything except the . I can't figure out how to
pass that directory
I'm writing a wrapper for RUM (RNA-Seq Unified Mapper). For those of you who
aren't familiar with RUM, it produces several output files. I'm trying to
capture 12 of those files in Galaxy.
Here is one of the 12 nodes:
All 12 nodes have similar syntax. When I try to run RUM from Galaxy, it's
ob
Hi Luciano,
I had a similar problem with our local instance of Galaxy. In our case, the
/tmp directory was filling up, causing the job to abort. We had Galaxy running
on a partition with tons of disk space, but the partition on which /tmp was
located had substantially less free disk space. Try
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