Hi,
try that in your galaxy directory:
GALAXY_RUN_ALL=1 sh run.sh --stop-daemon
GALAXY_RUN_ALL=1 sh run.sh --daemon
Cheers,
Bjoern
Hello,
I modified the Galaxy configuration file and would like to stop and
re-start the Galaxy process. Can you tell me how to do that?
Thank you.
Dear all,
I had problems configuring apache, which were solved by running apache
as user galaxy.
Is this an security issue? The server will only be use for galaxy.
Cheers,
Joachim
--
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and
Dear list,
When running Galaxy/Cloudman on Amazon (on Ubuntu 12.04), I run into the
following:
- I start a job with parallelism in the tool.xml file.
- Since I have use_tasked_jobs=True in universe_wsgi.ini, the job is
split and divided over the instances on EC2
- I change my mind, and click
I upgrade Galaxy to changeset 2531e085f262 and attempt to install freebayes
from the admin panel.
It installed the freebaye xml tool and appears in the tool panel but both
dependencies did not install (freebayes itself and samtools)
When I attempt to install either of them from the Tool shed
Hi Philip,
What do you have for the following configuration setting in the [app:main]
section of your universe_wsgi.ini file? The config setting for
tool_dependency_dir should be a valid subdirectory that is writable by the user
that starts your Galaxy server.
# Location for installing tool
Looks like I forgot to reset that value. So making progress... I can
install freebayes successfully (the front end timeout but it worked)
However, samtools fails with the following message in web worker log:
[localhost] local: sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile
Warning: local()
You should be able to click on the link for the samtools dependency from the
Installed tool shed repository page for freebayes. Clicking the link will
allow you to browse the INSTALLATION.LOG on disk and see what caused the
error. Your environment is probably missing some component required
Hi, Greg,
Thank-you so much for taking the time to answer my question. You
appear to be correct; I removed the virtual hosting configuration from
apache (I had some redirection configured to automatically forward
from port 80 to port 443), and this problem went away. I think I
should be able to
Hello Philip,
Philip Mabon wrote, On 08/29/2012 10:08 AM:
Looks like I forgot to reset that value. So making progress... I can install
freebayes successfully (the front end timeout but it worked)
However, samtools fails with the following message in web worker log:
[localhost] local: sed
That's pretty much what I had to do. Thanks for the full explanation so
others will know!
Philip Mabon
Senior Bioinformatician
National Microbiology Laboratory
Public Health Agency of Canada
On Wed, Aug 29, 2012 at 10:31 AM, Assaf Gordon gor...@cshl.edu wrote:
Hello Philip,
Philip Mabon
On Jul 16, 2012, at 6:14 AM, Geert Vandeweyer wrote:
Hi,
We have set up a local instance of galaxy-dist, using pbs-python to
communicate with our HPC. Everything is working great, except for the upload
functionality.
When I assign the upload1 to local:/// , uploading of small files
Great, I am glad it was useful.
Renaming the repository isn't needed, especially if you just have one
pull request open at a time. But there have been times I have had
maybe 4 or 5 open pull requests at once, so then it helps to keep
track of which repository maps to which feature or bug fix. If
Hi Team,
I had performed an upgrade of my Galaxy server and had experienced an issue
with some of the database / metadata files have been corrupted. I have found
instances where the dataset exists, but cannot be detected or read by galaxy
when attempting to analysis data from a history. In
On Jul 17, 2012, at 3:16 PM, Julian Pradinuk wrote:
Hi all,
I'm wondering if someone who has downloads working through apache (using
xsendfile) has encountered this error when downloading HTML files:
(13)Permission denied: xsendfile: cannot open file:
On Jul 18, 2012, at 5:02 PM, christopher fletez-brant wrote:
Hi Nate,
The test XML is:
tests
test
param name=input value=nullseq_test.bed ftype=bed /
param name=fold value=1 /
param name=gc_err value=0.02 /
param name=rpt_err value=0'02 /
param
Hi,
I have some code that makes a plot and creates a legend from a given
column name in the user's input data, which may have arbitrary column
names.
I'd like to create a dropdown list that has all the column names in
it, but I don't know the names beforehand; I won't know them until the
user
Hello,
I recently updated my instance of Galaxy Cloudman (using Amazon AWS) and I
have since not been able to run any jobs. I get the following error:
WARNING:galaxy.datatypes.registry:Error loading datatype with
extension 'blastxml': 'module' object has no attribute 'BlastXml'
Hi
The BLAST+ tools and the definition of the blastxml format were moved to
the tool shed. You should have seen a migration message during the update...
If you are not using these tools, perhaps you have a legacy reference to
the blastxml file which should be removed?
If you are using BLAST+
On Aug 24, 2012, at 9:48 AM, Mutlu Dogruel wrote:
Hi folk,
Do you know any method for reading (the extended) WSGI HTTP headers
from a custom tool?
If I put some debugging lines in
$galaxy/lib/galaxy/web/framework/middleware/xforwardedhost.py, I can
read the HTTP headers I want. But I
galaxy already has tool-dependencies which can be used.
for example, velvet's tool XML would include:
requirements
requirement type=packagevelvet/requirement
/requirements
the above will use the default version; or to specify a specific version:
requirements
requirement type=package
Hello all,
The September 2012 Galaxy Update is now
availablehttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09.
*Highlights:*
-
41 new papershttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09#New_Papers(a
new monthly high)
-
3 new public Galaxy
Hi Mohammad,
Don't forget to CC the mailing list ;)
It sounds like something has gone wrong with the update...
Peter
On Wednesday, August 29, 2012, Mohammad Heydarian wrote:
Hi Peter,
Thanks for your response.
I am not using any of the Blast tools, I have only tried using the filter
and
Hello all,
I am trying to get a Galaxy server configured to submit jobs to an
LSF cluster running version 7 update 2, generally CentOS/Redhat 5 systems.
I have the Galaxy host as a client in LSF, but when I tried to
configure/make/install the FedStage drmaa code, it errors out in the make
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