:10 AM PDT
To: Robert Baertsch baert...@soe.ucsc.edu, galaxy-dev@lists.bx.psu.edu
Hi Robert
Are you using the built in SQLite database ?
Hans-Rudolf
On 08/31/2014 01:27 AM, Robert Baertsch wrote:
I submitted 13 fastq files to tophat2 using DRMAA and got this error.
Is it fatal? BTW
Is there anyway to have galaxy not insert a row in the galaxy_session file for
failed logins. Every ping from china seems to generate a row in galaxy_session.
We have anonymous login turned off
Robert
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I submitted 13 fastq files to tophat2 using DRMAA and got this error. Is it
fatal? BTW: This is a super cool feature.
I’m running the following version of galaxy-dist.
changeset: 14212:91547729ffde
branch: stable
tag: tip
user:Nate Coraor n...@bx.psu.edu
date:
21, 2013 at 4:17 PM, Robert Baertsch baert...@soe.ucsc.edu
wrote:
Do you know a fast way to open large tiff files in galaxy ? The sniffer
recognizes the type, but clicking on the eyeball on a large 82mb file just
hangs.
Downloading the file and opening in preview does work but it is clunky
Does galaxy have an official place to store the character set for a text file?
I'm thinking of modifying the upload tool to prompt for the character set,
since it cannot be sniffed.
It should go in the hda/ldda metadata hash or extended_metadata for the dataset.
Any opinions?
BTW: everyone
histories are in their own frames. Still
investigating.
On Tue, Nov 5, 2013 at 12:06 PM, Robert Baertsch baert...@soe.ucsc.edu
wrote:
Carl,
Just to make sure I just deleted my tree and did a fresh checkout and tried a
third time. It happened all three times. I'm using a postgres database
if there is anything odd in the
console.
--
James Taylor, Associate Professor, Biology/CS, Emory University
On Mon, Nov 4, 2013 at 1:58 PM, Robert Baertsch baert...@soe.ucsc.edu wrote:
HI James,
I just pulled in the latest code to see how you changed from iframe to divs.
Very exciting update
, Jul 4, 2013 at 9:49 PM, Robert Baertsch
robert.baert...@gmail.com wrote:
Dan,
Do these readers support gzip files?
reader = fastqVerboseErrorReader
reader = fastqReader
Presumably you are writing a Python script using this library?
The answer is a qualified yes. Instead
, Robert Baertsch
robert.baert...@gmail.com wrote:
Peter and Dan,
I like the idea of replacing all open() with galaxy_open() in all tools. You
can tell the format by looking at the first 4 byes (see C code below from
the UCSC browser team). Is there some pythonic way of overriding open
, Robert Baertsch
robert.baert...@gmail.com wrote:
Peter and Dan,
I like the idea of replacing all open() with galaxy_open() in all tools. You
can tell the format by looking at the first 4 byes (see C code below from
the UCSC browser team). Is there some pythonic way of overriding open
data between workflow steps rather than
writing to disk? I admit that this will require some work but the first step
is to abstract the open.
On Jul 9, 2013, at 10:38 AM, Peter Cock wrote:
On Tue, Jul 9, 2013 at 5:53 PM, Robert Baertsch rbaer...@ucsc.edu wrote:
On Jul 8, 2013, at 3:33 PM, Peter
Dan,
Do these readers support gzip files?
reader = fastqVerboseErrorReader
reader = fastqReader
Do I have to define a special type in galaxy for gzipped files or will the
fastq type be ok?
Ideally, I would like to keep my files zipped and not have galaxy unzip them,
since they
Jun 15 09:08:09 2013 -0400
summary: Fix reports import issue reported by Lance,
https://trello.com/card/bug-in-reports-webapp-imports/506338ce32ae458f6d15e4b3/943
-Robert Baertsch
UC Santa Cruz
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ignore this last post
On Jun 27, 2013, at 3:09 PM, Robert Baertsch wrote:
I submitted a workflow that in turn submits a drm job to sun grid engine.
The queue had an error (probably due to a problem with automount).
Traceback (most recent call last):
File /inside/depot4/galaxy/lib/galaxy
instance. I committed a fix for those specific admin pages
yesterday, available in galaxy-central (stable as well as default branch).
-Dannon
On Thu, Jun 6, 2013 at 1:37 PM, Robert Baertsch baert...@soe.ucsc.edu wrote:
Hi Dannon,
I deleted the declaration to select2 in base.mako (line 42
areas in the admin panel) but if you need to temporarily fix a
single page to get things working you can execute
$('select').select2(destroy) in your javascript console.
-Dannon
On Tue, Jun 4, 2013 at 3:20 PM, Robert Baertsch baert...@soe.ucsc.edu wrote:
James,
I upgraded to the latest
specific admin pages
yesterday, available in galaxy-central (stable as well as default branch).
-Dannon
On Thu, Jun 6, 2013 at 1:37 PM, Robert Baertsch baert...@soe.ucsc.edu wrote:
Hi Dannon,
I deleted the declaration to select2 in base.mako (line 42) and that fixed
the problem for now
I upgraded to the latest galaxy-central and got an error when running migration
script 115 which lengthens the password field from 40-255.
It failed saying that the table migration_tmp already exists. I ran this
without any existing database so I don't think it is anything on my end. Any
When merging in the latest galaxy-central, I'm getting this error:
merging lib/galaxy/webapps/galaxy/controllers/library_common.py
merging lib/galaxy/webapps/galaxy/controllers/page.py
merging lib/galaxy/webapps/galaxy/controllers/user.py
merging run.sh
merging scripts/manage_db.py
abort: could
somewhere?
-Robert Baertsch
UC Santa Cruz
https://medbook.ucsc.edu
RUN1 - 9 seconds (1 sec to start, 0.2 sec to run , 2 sec metadata, 5.5 secs to
update client)
12:08:12.? main: log job on main thread
12:08:12.8 manager : galaxy.jobs.manager DEBUG 2013-03-30 12:08:12,867
(2308) Job assigned
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