I got this error which executing tophat2 in Galaxy:
Error in tophat:
[2013-02-13 02:02:43] Beginning TopHat run (v2.0.7)
---
[2013-02-13 02:02:43] Checking for Bowtie
Bowtie version:2.0.6.0
[2013-02-13 02:02:43] Checking for
Hi,
The problem has been solved.
There was a corruption within a user's email address, there was a character
that could not be decoded so it caused errors with permissions and the
datasets the user had uploaded.
--
Chris
On Fri, Feb 8, 2013 at 3:59 PM, galaxy-dev-requ...@lists.bx.psu.edu
Shall I replace:
/orig/path/hg19hg19hg19
/depot/data2/galaxy/bowtie2/hg19/hg19
with
hg19 hg19hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index
Yes, that's correct.
Finally, please email only galaxy-dev with questions about local installations;
Also, do I have make all the reference files executable?
No, that's not necessary.
Best,
J.
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists,
Ok sorry. I did that, but the output of splice junctions is empty. The
other outputs looks fine. What might be the problem?
Thanks,
Sachit
On Wed, Feb 13, 2013 at 1:20 PM, Jeremy Goecks jeremy.goe...@emory.eduwrote:
Shall I replace:
/orig/path/hg19hg19hg19
Error in tophat:
[2013-02-13 02:02:43] Beginning TopHat run (v2.0.7)
---
[2013-02-13 02:02:43] Checking for Bowtie
Bowtie version:2.0.6.0
[2013-02-13 02:02:43] Checking for Samtools
Samtools version:
If the other outputs are fine, then the problem is likely with your data and/or
your Tophat settings.
Good luck,
J.
On Feb 13, 2013, at 8:22 AM, Sachit Adhikari wrote:
Ok sorry. I did that, but the output of splice junctions is empty. The other
outputs looks fine. What might be the problem?
On Feb 12, 2013, at 11:23 PM, Anthonius deBoer wrote:
I think the hg clone link on the news brief is incorrect:
it states: hg clone https://bitbucket.org/galaxy-dist#stable
Probably should be hg clone https://bitbucket.org/galaxy/galaxy-dist#stable
Thanks for catching that, Thon. It's
I will try to reproduce. In the meantime, can you please check the JavaScript
console and forward along any errors that you see?
Thanks,
J.
On Feb 12, 2013, at 11:15 PM, Anthonius deBoer wrote:
Hi,
I had created a trackster vizualization that had not finished indexing yet,
Thanks, that's what I was missing.
On Wed, Feb 13, 2013 at 7:09 PM, Jeremy Goecks jeremy.goe...@emory.eduwrote:
Error in tophat:
[2013-02-13 02:02:43] Beginning TopHat run (v2.0.7)
---
[2013-02-13 02:02:43] Checking for Bowtie
On Jan 30, 2013, at 2:51 PM, Anthonius deBoer wrote:
Hi,
I continue to see this error in the logs, every time a jobs finishes:
galaxy.objectstore CRITICAL 2013-01-30 11:42:14,161
/mnt/ngs/analysis/svcgalaxy/DATA/job_working_directory/000/327 delete
error [Errno 39] Directory not empty:
On Feb 4, 2013, at 6:03 PM, James Boocock wrote:
Hi All,
I am currently working on a clustering interface for galaxy that will
hopefully enable users to pick the grid
in the tool form.
With tools that need access to files within the galaxy directory, I
have an idea to create a symlinked
Hello, Roy
There was a recent fix for this. Is this problem still occurring for you?
Thanks,
Carl
On Thu, Jan 31, 2013 at 10:17 PM, Blum, Roy roy.b...@nyumc.org wrote:
Dear Galaxy support,
In the last 24 hours we are unable to load files to the Galaxy server.
We tried doing so as guest
On Feb 5, 2013, at 4:29 PM, Carlos Borroto wrote:
Hi,
I would like to use Apache LDAP to authenticate a local toolshed.
Configuring community_wsgi.ini wasn't a problem and I can now login
into the local toolshed with my institution active directory
credentials. The same way I do for the
On Feb 7, 2013, at 2:29 PM, greg wrote:
I think I found the problem. The TMPDIR environment variable was set
to /tmp/5393732.1.f03.q for jobs galaxy was running. (I guess the
admins do this?)
SGE does this to create a job-specific temporary directory that it can clean up
after each job
On Feb 7, 2013, at 2:43 PM, Anthonius deBoer wrote:
That's very unfortunate...
I have a ton of tools and I guess now I have to create a package for them in
a local toolshed to update them in a running galaxy server?
In any case...The toolshed installation also does not work for me...I
On Feb 11, 2013, at 7:48 AM, Joachim Jacob |VIB| wrote:
Hello all,
After a *reboot* of our Galaxy server, the environment variables are set
correctly.
However, after *restarting* the Galaxy process on a running server, by
logging in as Galaxy and running the init script on CentOS as
On Wed, Feb 13, 2013 at 10:38 AM, Nate Coraor n...@bx.psu.edu wrote:
You'll need something here like:
Satisfy Any
Order deny,allow
Deny from all
Allow from your.galaxy.server
Thanks Nate!, this worked flawlessly. My work around was to point
galaxy to the toolshed paster
On Feb 12, 2013, at 11:17 AM, Sarah Diehl wrote:
Hi all,
I have problems with datasets that were linked into Galaxy data libraries (as
Admin: Add datasets, select Upload files from filesystem paths and Link
to files without copying to Galaxy). Those files cannot be looked at,
downloaded
On Feb 12, 2013, at 10:49 AM, Gaueko Erge wrote:
Hi,
I have followed, carefully, the instructions posted
in:http://wiki.galaxyproject.org/Admin/Data%20Integration
Yet, despite my best efforts when I get, say all exons from hg19 build and
try to their fetch sequences, galaxy tells me
On Wed, Feb 13, 2013 at 2:11 PM, Carlos Borroto
carlos.borr...@gmail.com wrote:
On Wed, Feb 13, 2013 at 10:38 AM, Nate Coraor n...@bx.psu.edu wrote:
You'll need something here like:
Satisfy Any
Order deny,allow
Deny from all
Allow from your.galaxy.server
Thanks Nate!, this
Carlos,
Sorry you're having difficulty here. I'm not able to help very much here
because I'm not familiar with the Galaxy remote user authentication process and
I don't have an environment in which to mess with it.
In case it helps, however, the Tool Shed uses the same code for remote user
Hi,I am continue to struggle with the proccess of killing jobs that run on the SGE cluster when deleting histories.I would assume that jobs get removed from the queue when a history they are part of is deleted but in most cases, the jobs stay on the cluster and are not killedI also never have
I'm getting this in the console...SharedContentScript::onBackgroundPageMessage: init {"oktaDomain":{},"settings":{"pluginFormFillCaptureEnabled":false},"matchedFullCredSitesNoPw":[]} log.js:1Uncaught TypeError: Cannot call method 'get' of undefined circster:6Uncaught TypeError: Cannot call method
On Wed, Feb 13, 2013 at 3:10 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Carlos,
Sorry you're having difficulty here. I'm not able to help very much here
because I'm not familiar with the Galaxy remote user authentication process
and I don't have an environment in which to mess with it.
Thanks Carlos,
I've added the following Trello card for this:
https://trello.com/card/toolshed-problems-installing-a-repository-from-the-tool-shed-into-galaxy-if-using-remote-user-authentication/506338ce32ae458f6d15e4b3/622
Greg Von Kuster
On Feb 13, 2013, at 3:25 PM, Carlos Borroto wrote:
Would this problem go away if I only used ONE webserver in my proxy setting and not use a balancer?I may not need it and if it means I could not use the toolshed effectively, it may be worth it not to use balancing..What i really need is the manager being balanced, since submitting a workflow with
Hi,I see this in the log file...this really "suc"ks :)ThonException in thread Thread-1:Traceback (most recent call last): File "/usr/lib64/python2.6/threading.py", line 532, in __bootstrap_inner self.run() File "/usr/lib64/python2.6/threading.py", line 484, in run self.__target(*self.__args,
Hello Thon,
This has been fixed in change set 8840:dde899d789b6.
Greg Von Kuster
On Feb 13, 2013, at 4:24 PM, Anthonius deBoer wrote:
Hi,
I see this in the log file...
this really sucks :)
Thon
Exception in thread Thread-1:
Traceback (most recent call last):
File
On Feb 13, 2013, at 4:12 PM, Anthonius deBoer wrote:
Would this problem go away if I only used ONE webserver in my proxy setting
and not use a balancer?
I may not need it and if it means I could not use the toolshed effectively,
it may be worth it not to use balancing..
No, because your
Interesting!But maybe it is not the manager that is the bottleneck, but which process is the one that takes the inputs from the webpage (or in the API) and prepares all the files that are produced by the workflows?I guess it is the MAIN server?THAT is the one that is the bottleneck I think
Thanks for the help, Björn. I will keep an eye on it when I go to merge.
Il giorno martedì 12 febbraio 2013, Björn Grüning ha scritto:
Hi Amanda,
the tools directory is also tracked and updated in mercurial. But only
the tools that are shipped with galaxy. If you have inserted your own
Hi there,
I am using my own Galaxy instance and since I updated, I can't see file of
several datatypes (for example the 'tabular' ) clicking on the eye icon.
Is that a problem linked to the new release ?
Cheers,
Mathieu Bahin
___
On Feb 13, 2013, at 6:16 PM, David Joly idj...@gmail.com wrote:
Hi!
Ok, I know many people had the same issue, but I just can't figure what's
going on. I'm quite new about using a local instance of Galaxy and I'm trying
to figure how to install a tool from the tool shed. Reading the
How old is the galaxy you're running? To use the main toolshed you'll need to
use a galaxy-dist release from December or later. After this point in time the
interface was standardized and is backwards compatible.
To update, you should be able to simply navigate to your galaxy-dist directory,
Mathieu,
To clarify -- is this after the new galaxy-dist release, or new code in
galaxy-central? And, is this *any* tabular file? Or just ones of a
particular size? (Files of 50 columns are handled as a special case, for
instance)
-Dannon
On Wed, Feb 13, 2013 at 11:29 AM, Mathieu Bahin
Hi,One very cool feature was to be able to search quickly for datasets using the search feature.You could continue to add terms until your search results in the correct set...It was basically doing an AND search for the terms you entered.This feature has seem to have disappeared?Now a search
Ok, one more step closer (I thought closing the browser would be enough to
restart galaxy, but obviously, I had to reboot the computer).
But now it says: ValueError: too many values to unpack
2013/2/13 Dannon Baker dannon.ba...@gmail.com
On Feb 13, 2013, at 6:16 PM, David Joly
This could be the problem, I just installed BioLinux 7 on my computer with
Galaxy running out-of-the-box...
However, it looks like they changed a few things, there is no .hg file and
no galaxy-dist folder. Can I update outside of mercurial?
2013/2/13 Dannon Baker dannon.ba...@gmail.com
How
I want to redirect all the output of Galaxy to another directory(actually a
external hard drive with full write access). How can I do that? Thanks
___
Please keep all replies on the list by using reply all
in your mail client. To manage your
Tophat2 output on accepted hits, deletions and insertions is fine
whereas splice
junctions output is only:
track name=junctions description=TopHat junctions
I am running tophat2 with hg19 reference genome? What might be the problem?
___
Hi Shantanu,
We are facing the same situation that migrating galaxy dataset to a new
location is needed. I am wondering if you have done it successfully? Would
be nice if you can share your experience with us.
Cheers,
D
On Fri, Nov 30, 2012 at 9:21 AM, Shantanu Pavgi (Campus)
I would like to enroll, galaxy-dev mailing list.
Regards,
Z. Oya Uyguner
Department of Medical Genetics
Istanbul Medical Faculty
Istanbul University
Bu elektronik posta ve beraberinde iletilen bütün dosyalar sadece göndericisi
tarafindan alinmasi amaçlanan yetkili gerçek ya da tüzel kisinin
you can change the location where all the dataset files are stored in
universe_wsgi.ini:
# Dataset files are stored in this directory.
file_path = database/files
if this is, what you want?
Regards, Hans-Rudolf
On 02/14/2013 05:40 AM, Sachit Adhikari wrote:
I want to redirect all the
Hi Thon
I can't help you killing the job on the clusterbut regarding the
admin section (and the database):
On very rare occasions, we do have jobs (which are not running anymore)
but are labelled as running on the Manage jobs page in the admin
section. Using the Stop Jobs option does
45 matches
Mail list logo
