Am Mittwoch, den 16.10.2013, 01:41 -0500 schrieb Eric Rasche:
Hi Bjoern,
On 10/16/2013 01:26 AM, Bjoern Gruening wrote:
Hi Eric,
Hello all,
I've been digging through the available galaxy tool config files and
have been unable to find a solution, so I bring my problem to you.
I
Hi,
About the last updates on DRMAA: now the job is submitted, it seems to
work. However, galaxy is restarting constantly... So it became very
unusable.
I hope you will fix this.
Regards.
2013/10/14 Rémy Dernat remy...@gmail.com
Hi,
After a big upgrade, I have an error when I submit job to
Hi,
I have discovered the following weird Galaxy behaviour. If one sets
log_actions = True
in universe_wsgi.ini
and tries to display the Saved Histories, then the Saved histories
don't show up.
The problem arises from ../lib/galaxy/web/framework/helpers/grids.py
line (around 230)
Hej
I am new to Galaxy. I am reading the documentation but could not really
find an answer . I would like to create a tool that when after executed on
a cluster the user should be able to interact with the running job. Get the
current output and make a plot and see how far the job has come.
Hello Devteam,
I've read through the fastx_readme regarding the barcode splitter. I know that
i'm supposed to modify the publicurl and basepath variables in order to
produce the necessary table. I've set the base path to a local folder but I
don't know what to use for the public url. I've
Hello Jonas,
I don't believe this is currently doable in Galaxy and it may be
difficult to add. I worry that some job/file/cluster configurations
Galaxy could be in might not even be setup in such a way that
intermediate files, standard output, etc... would not be available to
the Galaxy
This is not currently implemented, but the feature is listed as in
planning on Trello: https://trello.com/c/zZ02ln5a. I will link to this
request and encourage you to add your vote for the feature. It is
definitely something that multiple people are interested in and would
really enhance the
Hi Rémy,
Do you have some process that restarts Galaxy if it dies? It should not do
this itself. Is there anything being logged right before the server restarts
that indicates the problem?
--nate
On Oct 16, 2013, at 4:10 AM, Rémy Dernat wrote:
Hi,
About the last updates on DRMAA: now
Hi, Nikolai
This should have been fixed with commit 10200:fd4113962c32 to the stable
branch. What version are you using?
Thanks
On Wed, Oct 16, 2013 at 8:19 AM, Nikolai Vazov n.a.va...@usit.uio.nowrote:
Hi,
I have discovered the following weird Galaxy behaviour. If one sets
log_actions
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On 10/16/2013 01:51 AM, Bjoern Gruening wrote:
Am Mittwoch, den 16.10.2013, 01:41 -0500 schrieb Eric Rasche:
Hi Bjoern,
On 10/16/2013 01:26 AM, Bjoern Gruening wrote:
Hi Eric,
Hello all,
I've been digging through the available galaxy tool
Hello Shenwiyn,
We can confirm that the hg_g1k_v37.fa is currently unavailable. We are
working to correct this.
Meanwhile, the hg_g1k_v37.2bit files is available. This can be convert
to fasta using the tool twoBitToFa available from UCSC in the
downloads area, under source code,
Hi Lei,
You can download all at once or in two parts (for slower
connections):
iGenomes has been pretty good about using the exact same build as
released by the source with no changes for the GTF files, but I do
not know about the indexes - so do
Update:
We are hosting .2bit files as a standard on the rsync server, so this is
how to retrieve sequence data. No .fa files will be served.
The advantages are that the files are 25% smaller, the rsyncs are
quicker, and local/cloud users can easily convert to fasta format anytime.
I will
Hi Tim,
Were you able to fix your problem?
Thanks,
Sam
On Fri, Oct 4, 2013 at 1:05 PM, Nate Coraor n...@bx.psu.edu wrote:
Tim,
Just to be certain, if you have AJAX upload enabled, you'll see this
message after you click Execute on the upload tool:
Lei Yan,
I am very glad that this worked out! It looks like you have already
helped at least one other user and I am sure others to come!
We were discussing this internally while you were working. Updates to
the ready-loaded data on cloud instances will be getting a make-over in
the near
Thanks Jen and James so much.
Now it looks like I have fixed the problem about tophat_indexes_color,
because Tophat for SOLiD tool is running in my account (still running,
but not finished yet). Here is a summary:
- The hg19 index files for colorspace have been there, so I don’t need
to
On 10/16/13 5:49 PM, Lei Yan wrote:
Hope this can help somebody.
Me too! I'll try it ASAP.
LTR
--
Lawrence T. Reiter, Ph.D.
Associate Professor, Department of Neurology
855 Monroe Ave., Link 415
Memphis, TN 38163
901-448-2635 (Office)
901-448-7440 (FAX)
901-448-7443 (Lab)
e-mail:
Hi James,
I found this: http://bowtie-bio.sourceforge.net/manual.shtml
There are some Pre-built indexes in the right side of this page.
If I just need an hg19 index for colorspace, which index file can work for
us?
Thanks again.
Lei Yan
Center for Integrative and Translational Genomics
The
Hi Jen and James,
Thanks for your info.
Yes, we are already running a cloud instance (
http://galaxyclass.genenetwork.org/).
So if I can build the index for colorspace, then how to configure it?
And I didn’t find the “tophat_indexes_color” record in the Admin - “View
data tables registry”. Please
PS: I just tried running all the delete and purge scripts without further
paramters as described on
http://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20a
nd%20Datasets. However alls the dat files are still there in the /files/000
folder. How does one execute the scripts
Hi,
thanks for your help. Hope the update comes soon.
I have another small question. After I install bowtie2 and tophat2 and set
the paths using export PATH=$PATH:... the paths are added to the variable
but when I terminate and restart they're gone again. What should one do
here?
Best
Stan
Hello,
I have set up a galaxy instance and I'm trying to use Apache so that I can
access UCSC. I have the following set in my httpd.conf (below) file in Apache2
and I've altered the folioing in my universe_wsgi.ini file. When I launch
galaxy I no longer see my history. If it attempt to login
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