HI,
Thanks for the reply.
actually my server is not connected with the internet. Previously i
downloaded in another system with internet connection and installed to
server. now i gave internet connection to the server now i could connect to
it and download the python eggs.
Thanks
Sridhar
On
On May 2, 2013, at 12:54 PM, Peter Cock wrote:
Another even simpler change (which would also make a big
difference) is to actually have the name of the current
repository on the Upload a single file or a tarball page.
Thanks,
On Thu, May 2, 2013 at 9:32 PM, Greg Von Kuster g...@bx.psu.edu
On 2013-05-01 08:52, Greg Von Kuster wrote:
Hi Peter,
I created the following Trello card for this and things will be fixed as a
priority. Thanks for letting us know!
https://trello.com/card/toolshed-issues-with-functional-test-results/506338ce32ae458f6d15e4b3/823
On Wed, May 1, 2013 at
Hi,
This is an old topic now, but here is a little update (fork from Git / John
Chilton) of this code:
https://gist.github.com/remyd1/5524162
Regards
Remy
2013/1/8 Hagai Cohen haga...@gmail.com
This is really helpful,
Works great.
Thanks,
Hagai
On Mon, Jan 7, 2013 at 5:13 PM, John
Peter,
Yes, there are a few issues that are causing some repositories not to be
tested correctly. I've discovered the problem, but the solution will
require a bit of work. My goal is to have this resolved as soon as possible.
--Dave B.
On 5/6/13 05:10:57.000, Peter Cock wrote:
On
Hello all,
The May 2013 Galaxy Update is now
availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_05
.
*Highlights:*
-
the GCC2013 http://wiki.galaxyproject.org/GalaxyUpdates/2013_05#GCC2013
*early registration deadline is 24
Hi Galaxy team,
I am having problems with taxonomy information fetching.(Metagenomic
Analysses-Fetch taxonomic representation).
According to the following link
http://dev.list.galaxyproject.org/quot-Fetch-taxonomic-representation-quot-DOESN-T-WORK-td4565489.html
I have installed libraries from
Hi all,
I am trying to set up a Galaxy cluster using the LWR runner. The nodes have
a shared filesystem and in universe.wsgi this parameter is set :
job_working_directory = /mnt/shared
...
clustalw = lwr://http://192.168.33.12:8913
this folder has been chown-ed to the galaxy user, and
Hello Dr. Krampis,
At the present, the LWR is most valuable when there is not a shared
file system between the server executing the jobs and the server
hosting Galaxy. In this case you seem to have a shared filesystem so I
would think setting up something like sun grid engine to manage the
jobs
Hi Dannon,
We did update our galaxy development instance to the latest distribution
(April 1st).
Unfortunately, because of some LDAP issue (we are testing to implement
LDAP authentication at the same time) I didn't had time yet, to test if
this would solve the markupsafe issue.
As soon as I
Hi John,
thanks for the quick reply! It is actually a virtual cluster using virtual
machines
with VirtualBox, which are brought up via Vagrant (www.vagrantup.com) - that
also sets up the shared filesystem. I chose LWR for the reason that it not a
real
cluster, and needed something lightweight
Hello,
I figured out the place where the cookie gets set in Galaxy and then add
secure to that. Apache configuration didn't work well.
added the following code into function set_cookie in:
lib/galaxy/web/framework/__init__.py
*def set_cookie( self, value, name='galaxysession', path='/',
On Thu, May 2, 2013 at 10:24 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, May 2, 2013 at 7:16 AM, Ira Cooke iraco...@gmail.com wrote:
Hi all,
I've written a script to help deal with the problem of maintaining toolshed
tools
across multiple toolsheds (eg test and release)
The
Thanks James!
I have pulled the recent changes to my repository and this is working fine.
I have tested with creating a new user
and I tried to login with the recently created user and this works fine at
my end. The entry looks like as follows:
galaxy=# select username,email,password from
Hello all,
This is to report a usability bug with workflows - specifically the curiously
separate handling of Published Workflows in the user interface.
1. Log into your Galaxy account,
2. On the top ribbon, click on Shared Data, Published Workflows,
and make a note of the entries.
3. Return to
Hi, I am wondering what I can do to add more genomes to this list
(hopefully this image will make it through the mailing list). I am
importing fastq files from a MiSeq run. We are using a modified version of
Galaxy called Tron.
Everything I see on the wiki is about adding custom reference
On Mon, May 6, 2013 at 9:35 AM, Krampis, Konstantinos kkram...@jcvi.org wrote:
Hi John,
thanks for the quick reply! It is actually a virtual cluster using virtual
machines
with VirtualBox, which are brought up via Vagrant (www.vagrantup.com) - that
also sets up the shared filesystem. I
Opps that last message got sent before I meant to.
I meant to finish saying that this file would need to be changed:
https://bitbucket.org/galaxy/galaxy-central/src/default/lib/galaxy/jobs/runners/lwr.py#cl-80
queue_job() will likely need to skip everything to do with the
FileStager class and
On Fri, Mar 15, 2013 at 2:50 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Peter,
I've looked over the wiki and as far as I can see, 'when' tags used inside
'conditional' tags only work on another input variable's values.
I would like to be able to do is a
Dear Sir or Madam,
I hope this reaches you well. Lately, I have been trying to use tophat and then
use bowtie on Galaxy project to create an aligned BAM file. The original data
came from a SRA file that I have acquired from the Japanese DNA Databank. This
SRA was then converted to FASTQ using
Deeps,
It does not appear that you have installed taxBuilder on your system.
What commands did you use to compile it on your system?
If you type 'which taxBuilder' it should return no results (assuming
installed incorrectly). You will need to 'make clean' then 'make all'
then manually move the
Hi Team,
I urgently need to resize the data partition on my galaxy cloudman instance
without loosing anything. I notice that there a gui on the cloudman admin page
that will allow me to increase it to 1000GB. If I use that will it restart all
of the processes? I need to maintain this as a
Hi Iry,
This should work, I use it regularly. Just make sure you're not ssh'ed in
and 'in' /mnt/galaxyData or anything like that. There's not really another
way to do this that I'd recommend trying if you need the instance to
continue working for something tomorrow.
Let me know if you have any
i.e. Published Workflows are hidden or separated away from the others.
This appears to be a design choice (like shared datasets they must be
imported before use), but if so this could be clarified as follows:
This was a very old design choice that will be revisited in the (hopefully
near)
On Mon, May 6, 2013 at 9:55 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On May 2, 2013, at 12:54 PM, Peter Cock wrote:
Another even simpler change (which would also make a big
difference) is to actually have the name of the current
repository on the Upload a single file or a tarball page.
Hello all,
I've noticed a couple of weaknesses in the current revision view
for the Tool Shed.
First, the commit comment is not shown - this would make sense
next to the revision number and above the diffs.
Second, there is no easy way to jump to the next/prev revision,
you must first go back
Hi Dannon,
I will give it a shot. Are you familiar with the load balancer and how to make
it work? Or the auto scaling feature?
Thanks,
Iry
From: Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com
Date: Monday, May 6, 2013 2:06 PM
To: Iry Witham
I seem to be in feedback mode: another little rough edge in Galaxy:
When using a tool in Galaxy, at the end of the parameters there is a nice
eye catching blue button labelled execute.
When running a workflow in Galaxy, the equivalent button is plain grey
and reads Run workflow. I think it would
Hello all,
I've recently started sharing some sample workflows on the Galaxy Tool Shed,
http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
When writing a Galaxy tool we have a lot of flexibility within the help
tag
Hi Dannon,
I have attempted the resizing. I clicked on the disk and set it for 1000GB.
The instance restarted, but the volume remains at 100GB. Is this due to the
lack of disk space? I don't see a snapshot when I look at the AWS console
after the restart. Any ideas?
Thanks,
IRy
From:
Thanks for the suggestion -- this style should definitely be applied in
both places and I've done so in 9659:bcb6e71eda61.
-Dannon
On Mon, May 6, 2013 at 2:30 PM, Peter Cock p.j.a.c...@googlemail.comwrote:
I seem to be in feedback mode: another little rough edge in Galaxy:
When using a tool
So you have a cluster with 9 instances and you're using ec2 load balancer
with all of them to divert traffic?
On Mon, May 6, 2013 at 3:56 PM, Iry Witham iry.wit...@jax.org wrote:
I have setup a load balancer, but it shows that only 1 of 9 instances
are 'In Service. I have set the health
I was not clear how the load balancer worked in this instance, but my goal was
to improve performance. I am not sure this was the correct use, but it seemed
to work.
From: Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com
Date: Monday, May 6, 2013 4:12 PM
To: Iry Witham
Ahh, ok. So, unfortunately Cloudman isn't designed to be used with a load
balancer (at least at this point). In any given cluster you have exactly
one master node and all of the rest are workers (which do not run web
processes, hence the 1/9 health).
What was slow that you were trying to
I did add nodes about the same time I setup load balancing so that was likely
the fix. I will definitely set the head node not to run jobs.
Thanks,
Iry
From: Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com
Date: Monday, May 6, 2013 4:19 PM
To: Iry Witham
Ok, cool. It's worth noting that worker nodes are completely disposable
and that if there are any not running jobs at the top of the hour (when
billing happens) it's a waste. What you may want to do, at least until the
event tomorrow, is scale back down to 1 master and 1 worker node and turn
on
I thought this would be transparent to the users instead of forcing
to reset the password.
Two thoughts... but please consider that I might not know what I am
talking about, and that these might not be good ideas ...
(1) James' implementation supports two hashing schemes in the table.
Hi Peter,
Thanks for your message - these should't take long once I'm back to typing with
2 hands. I've added the following Trello card for this.
https://trello.com/card/toolshed-page-improvements-and-fixes/506338ce32ae458f6d15e4b3/839
Greg
On May 6, 2013, at 2:17 PM, Peter Cock wrote:
You can add genomes in this file:
$GALAXYROOT/tool-data/shared/ucsc/builds.txt
Note that without related files (e.g. genome sequence, indices for mapping),
the build information isn't very useful. However, with an entry in this file,
you can link it to other resources when they become
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