This Galaxy speed and production question reminded me that I have been meaning
to raise the following question on the list:
For a single job (workflow item), It seems like there is a 20 second lag
before the job is launched. It gives the impression that Galaxy is slow and
unresponsive (in
Hi
I presume the best way to optimise your current problem is to evaluate whether
you really need to groom your data!? If its old data presumably yes, but if it
is recent data in Illumina 1.8+
encoding(http://en.wikipedia.org/wiki/FASTQ_format) it is not necessary
speedup 100% :-)
Groom
Hi,
how do I get tools from one local toolshed (or the main galaxy toolshed)
into another tool-shed? Is it possible to clone the content of a complete
tool-shed - all repositories
at once into another tool-shed?
Can I then import all the tools at once into a local galaxy instance?
We have a
This should be resolved in changeset 1ac27213bafb in galaxy-central. Thanks
for pointing this out!
-Dannon
On Dec 3, 2012, at 11:37 AM, Marc Logghe marc.log...@ablynx.com wrote:
Hi,
The conf of the parameters in question looks like this:
param name=project1 type=select label=Project
On Dec 4, 2012, at 9:30 AM, Andreas Kuntzagk andreas.kuntz...@mdc-berlin.de
wrote:
I see that this issue came up before by Oleksandr Moskalenko in October but
was unresolved then.
Is there a workaround now?
regards, Andreas
The velvet wrapper is not going to be usable for real user jobs
Hi Franco,
The server error is thrown when your file named tool_data_table_conf.xml.sample
is parsed. The content of this file is the following.
!-- Locations of indexes in the bisulphite conversion --
table name=bismark_indexes comment_char=#
columnsvalue, dbkey, name, path/columns
Hi Alex
I look the page of wikipedia, but I have a little confused. We sequenced with
solexa. I paste a read of my data, can you tell me whether I need run Groom?
The read is like this:@HWUSI-EAS1734_0003_FC620JEAAXX:8:1:1174:9013#0/1
Hello all,
I am having issues downloading HTML files from Galaxy the same as is
described in this email chain:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-August/010965.html
I am getting the error (13)Permission denied: xsendfile: cannot open file:
On Dec 4, 2012, at 10:52 AM, Josh Nielsen wrote:
Hello all,
I am having issues downloading HTML files from Galaxy the same as is
described in this email chain:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-August/010965.html
I am getting the error (13)Permission denied: xsendfile:
On 04/12/12 16:52, Josh Nielsen wrote:
I am getting the error (13)Permission denied: xsendfile: cannot open file:
/basedir/galaxy_data/database/tmp/tmp8iEccn/library_download.zip which is
indeed a basic filesystem permissions issue. The problem is that the
permissions created for that directory
Hi Nate,
Thanks for the reply. No I hadn't thought to add anything to
/etc/init.d/galaxy itself. It is a short enough script that I can paste it
below. What would I need to do to edit it with umask settings?
Also I should note, changing the umask in the PAM files actually did change
the default
Hi Ido,
On Dec 4, 2012, at 10:26 AM, Ido Tamir wrote:
Hi,
how do I get tools from one local toolshed (or the main galaxy toolshed)
into another tool-shed? Is it possible to clone the content of a complete
tool-shed - all repositories
at once into another tool-shed?
Not at the current
Hi,
You can use fastQC to find out what is the quality encoding of your sequences
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Alternatively, you can also use this script:
http://www.uppmax.uu.se/userscript/check-fastq-quality-score-format
David
Date: Tue, 4 Dec 2012 23:41:27
Hello Franco,
The tool dependency installation fails due to BEDTools.v2.17.0.tar.gz
extracting into a directory named bedtools-2.17.0, rather than
BEDTools.v2.17.0. Also, you following tag is not optimal since it assumes a
specific os platform.
action type=shell_commandcp bin/*
Hi Ted
You can cut down the lag by 5 secs if you delete the time.sleep( 5 )
in '~/lib/galaxy/jobs/manager.py' ( line 155)
(see also my e-mail from Nov 7: in this email conversation:
Hi Paul,
Thanks for replying. Interestingly I've never dealt with filesystem ACLs
before and I didn't even know that ext3/4 systems had that feature.
Here is my output from those commands:
bash getfacl tmp8iEccn
# file: tmp8iEccn
# owner: galaxy
# group: galaxy
user::rwx
group::---
mask::rwx
Hi Adam,
I believe this is related to the invalid xml definition in your repository's
tool_data_table_conf.xml.sample file which I discussed in a previous reply.
Greg Von Kuster
On Dec 4, 2012, at 8:08 AM, Adam Carr (NBI) wrote:
Hi,
I hadn't caught this as I posted my query to the list,
On Dec 4, 2012, at 11:23 AM, Josh Nielsen wrote:
Hi Nate,
Thanks for the reply. No I hadn't thought to add anything to
/etc/init.d/galaxy itself. It is a short enough script that I can paste it
below. What would I need to do to edit it with umask settings?
Also I should note, changing
On 04/12/12 17:35, Josh Nielsen wrote:
Hi Paul,
Thanks for replying. Interestingly I've never dealt with filesystem ACLs
before and I didn't even know that ext3/4 systems had that feature.
Here is my output from those commands:
bash getfacl tmp8iEccn
# file: tmp8iEccn
# owner: galaxy
#
Great. I'll give those ideas a shot to see if it gets me anywhere.
P.S. You referenced in the email that I linked to a fix in the next release
of Galaxy. Is that out yet or still in development?
-Josh
On Tue, Dec 4, 2012 at 10:44 AM, Nate Coraor n...@bx.psu.edu wrote:
On Dec 4, 2012, at 11:23
On Dec 4, 2012, at 11:57 AM, Josh Nielsen wrote:
Great. I'll give those ideas a shot to see if it gets me anywhere.
P.S. You referenced in the email that I linked to a fix in the next release
of Galaxy. Is that out yet or still in development?
The fix was in the September 7, 2012
This isn't (at least at first) Pause/Resume as you might be expecting - where
you could manually pause a currently running job and continue it later. What
we're doing at least in the first pass is using 'Paused' as an internal state
that jobs only go into in two scenarios:
1) User quota is
It seems old Illumina encoding 1.5
So yes some tools requiring the fastqsanger would need grooming.
If you are up to programming you can seriously speed this up by using a
precalculated transfer or hash table.
That way you do not have to do any calculation but just translate each quality
line
Thanks Dannon.
No worries. Yes my interest was different. On a private local Galaxy, or a
private Cloud one, sometimes a job seems to be going awry, taking forever
etc. I was interested in the ability to suspend it, check what's wrong,
maybe fix it, maybe resume or cancel the job.
Rgds,
Greg E.
Dear Galaxy devs,
We are in the process of deploying Galaxy internally here at AgResearch, and I
am currently installing required dependencies. My question relates to RPy. It
seems that RPy2 is not yet supported by Galaxy, so we're stuck with RPy 1.0.3a,
and this seems to have rusted quite
I don't have a velvet or a submit-jobs-as-user environment setup so I
cannot test this, but it seems like this should have a an easy fix.
Can someone who is experiencing the problem try the attached patch or
has something like this been tried and there is some other problem?
-John
(09:43:01 AM)
Hi,I am trying to figure out how to run galaxy distributed over several physical servers, with different IP addresses...The wiki on scaling and load balancing only speaks of balancing on the same physical server, but does not address how to put a handful of managers on a different physical
Hi Shea,
This is a reasonable feature so we'll add it on the todo list. To make the
search for all untagged resources easier, did you have a list of the ones
that are currently not getting tagged?
Thanks,
Enis
On Tue, Dec 4, 2012 at 7:34 AM, Shea Lovan shea.lo...@lscg.ucsb.edu wrote:
We are
Got this when trying to install GMAP from the tool shed...Any ideas?Error Traceback:View as: Interactive|Text|XML(full)⇝KeyError:
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