Dear Galaxy users
I am trying to cut a tab delimited file using the cut option under text manipulation. When the columns I wish are cut out, the resultant file contains only '.' (dots) where the data was in the previous file.
Any ideas how to resolve this problem?
I can't find out how to use the dropdown "User type" which is displayed
after I select User > Register in the start page of Galaxy. Do I have to
define the types myself? Are they pre-set? The dropdown menu just says
"Select one", but the options are empty.
Thank you in advance
Nikolay Vazov, PhD
Research Computing Centre - http://hpc.uio.no
USIT, University of Oslo
I recently encountered a problem when trying to run Cufflinks on eight BAM
files on our galaxy instance (via the multi-input toggle) and received the
error: "Unable to run job due to a misconfiguration of the Galaxy job
running system" for some, but not all, of the cufflinks jobs that appear in
the history. These particular BAM files were copied over from the history of
a larger workflow where they were successfully run through cufflinks. In the
case of the problem workflow run, the cufflinks jobs are all successfully
submitted to Torque PBS and continue to run and finish but many have this
error displayed in the History. The jobs with the error displayed fail to
copy files from the working directory to the database directory despite
running to completion. We recently updated to galaxy-central changeset
6131:be6c89c33639. I have seen this error multiple times for this workflow,
even after restarting galaxy. Does anyone have any ideas of what might be
Thanks for any help,
Can we introduce new file types via tools in the tool shed? It seems Galaxy can load them if they are in the datatypes configuration file. Does tool installation automate the editing of that file?
Sr. Staff Software Engineer
9885 Towne Centre Drive
San Diego, CA 92121
I've again moved this back to the galaxy-dev list. Please reply to this
list and not galaxy-user.
Yan Luo wrote:
> Dear Nate,
> Thanks for your quick response. I appreciate, it is very important for us to
> use it. We have problem recently.
> (1) In fact, I can't find the file "paster.log". The problem is that
> recently we expanded our gluster(Linux sever) and did the rebalance that has
> some bugs. Some of files permission have been changed. So we can't use
> User/register righr now, when we tried, we got the sever error, do you have
> any idea how to fix it? (we can change the ownships/read and write
> permission for some files manually, but we don't know which files and where
> they are?)
If you are executing run.sh without the --daemon flag, the output will
go to whatever terminal window you started Galaxy in, not to a file.
You'll want to make sure that all of the files under Galaxy's root
directory are owned by a single user, which is the same user which
starts and runs the Galaxy process.
> (2) We want to reboot the Galaxy, should we first stop and start as
> $ sh run.sh --stop
> $ sh run.sh
The full command to stop would be `sh run.sh --stop-daemon`, but that
only applies if you originally started Galaxy with `run.sh --daemon`.
> Is there any difference if I use "-daemon" flag? Last times, my colleague
> started using "./run.sh". How to stop it?
> If "$ sh run.sh --stop" doesn't work (I didn't try yet, ), how can I find
> the process (Linux) that is running by Galaxy and kill it?
The --daemon flag runs Galaxy in the background and redirects its output
to paster.log. Without the --daemon flag, the process stays connected
to the terminal in which you start it.
Since Galaxy wasn't originally started with the --daemon flag, you'll
need to find the process, either by locating the terminal window in
which it was started (possibly by your colleague) and then hitting
Ctrl-C, or by using the `ps` command (e.g. `ps auxwww | grep python`)
and killing the Galaxy process. It usually looks something like:
nate 18213 0.9 0.4 438844 146260 pts/7 Sl+ 10:47 2:30 python ./scripts/paster.py serve universe_wsgi.ini
So you would do:
% kill 18213
> (3) Could you please let me know if there is a default administrator
> user/password for galaxy. I want to add an administrator user, how can I do
> According to the instruction, I will change a line of "universe_wsgi.ini" as
> follows. How can I set/get my password?
> admin_users = yan.luo(a)email.com
There is no default. Any users set in admin_uesrs will be
administrators. If the account specified in admin_users does not yet
exist, you can simply create it. Once created, that account will be an
> (4) I found our "universe_wsgi.ini" contains the following setting, should I
> remove "#" before this line, stop and start galaxy?
> #allow_user_creation = True
No, True is the default setting so with it commented it is still set to
> I plan to restart our galaxy, if it is possible, could you please let me
> know your phone #? I can call you sometime today, or if you prefer, I can
> give you my phone #.
Unfortunately, we don't have the resources for phone support. We'll be
happy to help via email as much as possible.
> Looking forward to hearing from you.
> Best Wishes,
> Yan Luo, Ph.D.
> On Thu, Feb 10, 2011 at 10:01 AM, Nate Coraor <nate(a)bx.psu.edu> wrote:
> > Hi Yan,
> > I've moved this discussion to the galaxy-dev list since it pertains to a
> > local installation of Galaxy.
> > Responses to your questions follow, in-line.
> > Yan Luo wrote:
> > > Dear Sir,
> > >
> > > (1)We installed Galaxy, but recently the user can't registered and got
> > the
> > > following error, how can we fix it?
> > >
> > > Sever error
> > > An error occurred. See the error logs for more information.(To turn debug
> > on
> > > to display ...).
> > Since debug = False in universe_wsgi.ini, you should be able to find a
> > more detailed error message in the log file. If starting Galaxy with:
> > % sh run.sh --daemon
> > The default log file is 'paster.log' in Galaxy's root directory.
> > > (2) Could you please let me know if there is any command to stop galaxy?
> > If starting with the --daemon flag (as above), you can use:
> > % sh run.sh --stop-daemon
> > If running in the foreground, you can use Ctrl-C to terminate the
> > process. There is a recent bug whereby Ctrl-C is ineffective on some
> > platforms under Python 2.6 - in this case you will have to kill/pkill
> > the process manually. We are working on a fix for the latter.
> > > (3) If I reset universe_wsgi.ini file and want to set an administrator
> > > user(I can add a line in the above file), how can I get the password?
> > Should
> > > I stop galaxy(See question 2) first? then run "./setup.sh" and
> > "./run.sh".
> > setup.sh would have only been necessary prior to running Galaxy the
> > first time, however, this step has recently been removed. If you are
> > referencing documentation that still refers to setup.sh, please let us
> > know so we can update it - I did notice this was still on the
> > "Production Server" page, so I removed it from there.
> > You no longer need to run setup.sh at all.
> > > (4) If I run "setup.sh", will a new file "universe_wsgi.ini" be
> > generated?
> > > if I want to change this file,should I edit it before "run.sh" and after
> > > "setup.sh". Is it right?
> > setup.sh and its replacements in run.sh and the Galaxy application
> > itself never overwrite files, they only create files from sample files
> > if they do not exist.
> > > (5) I read some of your docs, command "sh setup.sh"(sh run.sh) and
> > > "./setup.sh"(./run.sh), which one is correct under Linux?
> > Both syntaxes are effectively the same in most cases.
> > --nate
> > >
> > > Looking forward to hearing from you.
> > >
> > > Best Wises,
> > >
> > > Yan Luo, Ph.D.
> > > NIH
> > > <
> > http://int.ask.com/web?siteid=10000861&webqsrc=999&l=dis&q=By%20the%20way,
> > >
> > > _______________________________________________
> > > galaxy-user mailing list
> > > galaxy-user(a)lists.bx.psu.edu
> > > http://lists.bx.psu.edu/listinfo/galaxy-user
Hi, I updated my test server today and everything seemed fine. I added
a new library item via a URL. After that my history panel displays
"Internal Server Error" and I am getting the error below in paster.log:
Any ideas how this has occurred and if there is a fix?
Exception happened during processing of request from ('184.108.40.206', 63227)
Traceback (most recent call last):
"/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in
File "/usr/lib/python2.6/SocketServer.py", line 320, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.6/SocketServer.py", line 615, in __init__
"/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 432, in
File "/usr/lib/python2.6/BaseHTTPServer.py", line 329, in handle
"/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 427, in
"/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 290, in
"/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 125, in
"Content returned before start_response called")
RuntimeError: Content returned before start_response called
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
I am running the example_watcher_folder.py API script and it
intermittently fails to run a workflow on a file dropped into the import
directory (the file is imported and the workflow starts running, but its
jobs hang or fail). Galaxy uses a condor dramaa job runner. When I look
at the galaxy script being run by condor, it sets the PYTHONPATH and
then executes the following command, which also fails at the command line.
--column=7 --style=num --order=DESC
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/tools/filters/sorter.py", line 15, in
from galaxy import eggs
ImportError: No module named galaxy
How can I resolve this error? I would like to be able to test such
commands at the command line, as well as ensure that galaxy workflows
Sorry to bother you guys with such a simple thing. I'm quite new to the terminal and command line etc. so downloading and getting Galaxy running on my PC was a voyage of discovery! Anyhow, I have it, it's alive.......... just can't get any data in!
Have made myself an Admin User to create a data library, I point the importer at the files and it starts but never stops and remains at 0bytes. Have I forgotten to set something up?
Surely I can just dump all my files in a folder in the right place and go get it when I need it. Can't seem to find an idiots guide for setting this up for a local install (just me and my computer). Any pointers or helpful threads would be great.
Sent from my PC
I'm a systems administrator for an HPC cluster, and have been asked by a
faculty member here to try to get galaxy to work on our cluster.
Unfortunately, there are one or two outstanding questions that I can't
seem to find the answer to, and I'm hoping someone here can help me out.
In particular, is galaxy, and the PBS runner specifically, capable of
submitting jobs under specific user names? Essentially, if I set up
galaxy to push jobs to our cluster, will they all show up under one user
credential (eg. the "galaxy" user), or can we set it up so that the user
logged into galaxy, is used to submit the job?
This one is kindof a show-stopper, since our internal policies require
that all jobs have a specific user credential, with one person per username.
Fulton Supercomputing Lab
Brigham Young University