Karl,
For the URL you're pasting, is it the full path to a file in your s3 bucket,
including the protocol (http://) ? For galaxy to recognize that it needs to
pull from a URL rather than the contents of the box, you need to use the full
string.
-Dannon
On Mar 14, 2011, at 4:40 PM,
Keith,
We're currently experiencing a small issue with the main galaxy server. If you
could wait a while and then retry, it should be fully functional again soon.
-Dannon
On Mar 25, 2011, at 11:01 AM, Keith E. Giles wrote:
I keep getting a SERVER ERROR message. Is galaxy down, or is this
Yes, you can copy datasets to other histories, no need to re-upload. To do
this, click on Options in the history panel, and then Copy Datasets. From
here, you can pick a source history (defaulted to the current active history),
select the datasets to be copied, and then choose a destination
=== Please use Reply All when responding to this email! ===
As a first step, please confirm an exact line count for the files. See the
Line/Word/Character count tool in the Text Manipulation section to do this.
If the estimate is significantly off, please share the history with me and I'll
Makais,
Any type of command line tool, whether script or a binary executable, can be
used by Galaxy as long as it's properly installed on the system and accessible
to the Galaxy user.
See
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Ccommand.3E_tag_set
for more details on
Makais,
Any type of command line tool, whether script or a binary executable, can be
used by Galaxy as long as it's properly installed on the system and accessible
to the Galaxy user.
See
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Ccommand.3E_tag_set
for more details on
Arthur,
There is no zoom for the main editor window, though you can use(and resize) the
little mini view in the bottom right corner to move around the workflow
quickly. You could also use the browser-level zoom (in Chrome and Firefox, at
least) to see much more at a time.
-Dannon
On Oct
Hi Marc,
Yes, if you change Bowtie settings to use from common to full, you'll see the
entire parameter list, including Number of mismatches for SOAP-like alignment
policy (-v):
-Dannon
On Oct 27, 2011, at 8:40 AM, KNIGHT M.R. wrote:
Hi, is it possible to run Map with Bowtie for Illumina
I see in your screenshot that the security group is only listed as default.
Have you created the required security group as described in
http://wiki.g2.bx.psu.edu/Admin/Cloud ? If so, make sure you select that
security group when you launch the instance, and my guess is that it'll solve
your
Toqa,
Just to make sure I've understood your question: the problem is that a tool
that you're trying to wrap doesn't provide a way to specify a particular output
filename? Take a look at the from_work_dir attribute of a data element.
Or are you asking how to define outputs in general? For
and I am interested in this one only
..._CNTGS_DIST0_EM20.txt
any other method to overcome such problem
I have presentation tomorrwo. hope things will work fine.
Thank you,
From: Dannon Baker [dannonba...@me.com]
Sent: Monday, December 05, 2011
Changlong,
Lastz (and many other tools) allow you to select a reference from your history
instead of picking one of Galaxy's built-in references. To do this, upload
your reference and then when you run Lastz select in your history for the
reference location, and pick your uploaded file as the
Greg-
When you make changes to the EBS volumes of a galaxy cloudman instance and
choose 'persist' from the admin panel, an EBS snapshot is taken. The next time
you start an instance up, instead of creating the EBS volume from the base
snapshot that we distribute, it is created from your own
, mailing list wrote:
Thanks. So if I just want to run my own program that uses SGE, it
sounds like I shouldn't need a Galaxy instance. Is that right?
Does the storage space parameter control how much space is at
/mnt/galaxyTools?
-Greg
On Tue, Jan 10, 2012 at 2:50 PM, Dannon Baker
It looks like you're trying to restart an existing cluster (same cluster name)
that previously had galaxy included. Is this the case? If so, you'll need to
start it in the same availability zone as the existing volumes.
On Jan 10, 2012, at 3:03 PM, mailing list wrote:
The page seems to be
permanently.
-Dannon
On Jan 10, 2012, at 3:18 PM, mailing list wrote:
Yes, I did use the same name. I thought once I terminated everything
would be gone.
So how do I make a clean start?
Thanks,
Greg
On Tue, Jan 10, 2012 at 3:08 PM, Dannon Baker dannonba...@me.com wrote:
It looks like
, 2012 at 4:16 PM, Dannon Baker dannonba...@me.com wrote:Sorry, I should have specified before -- /mnt/galaxyData is automatically persisted, as it is assumed (and used behind the scenes in the case of a Galaxy Cluster) that this is where data will be kept. It's only /mnt/galaxyTools or /mnt
Ateeq,
The preferred method for uploading large files (that aren't already hosted
somewhere) is FTP. See the instructions here:
http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP
We don't generally provide specific analysis pipelines, rather the tools for
composing them, though you're
Yes, galaxyData is the only persistent volume you have in your data only
cluster, so everything should go there. SCP should work for getting data
there, unless the file is already hosted somewhere in which case wget is
probably a better choice.
And yes, FTP is configured specifically for
?? but seems to result in 1 Megabyte. Can I set
it to 1m, or 1g ?
Can't see how to restart nginx yet.
Thanks,
Greg E
On Mon, Jan 23, 2012 at 8:18 PM, Dannon Baker dannonba...@me.com wrote:
Hi Greg,
This is a problem with the default client_max_body_size option in nginx being
that in my Cloud setup than instruct my (not
very computer keen) wet-lab Proteomist clients how to use a subsidiary FTP
package, easy though that is. But I'll try the FTP approach too for
compariosn.
Thanks,
Greg E
On Mon, Jan 23, 2012 at 8:58 PM, Dannon Baker dannonba...@me.com wrote
Hi Jiwen,
The way the filter expression evaluates, you need to specify that you're
matching on the string '19', and not the numerical value 19. Everything should
work if you rerun with the filter condition:
c1=='19'
Thanks!
Dannon
On Feb 1, 2012, at 9:56 AM, 杨继文 wrote:
Hi All,
I got a
Jiwen,
After purging datasets, the history size update has a bit of a delay. Let us
know if you find that after a while it hasn't recalculated to what you expect
the value to be.
-Dannon
On Feb 1, 2012, at 4:21 PM, 杨继文 wrote:
Hi all,
First I would like to thank you for your fast replies
On Feb 10, 2012, at 3:28 AM, David Castillo wrote:
• I haven't been able to 'Edit' Workflows like in the public server, I
have been able to create them, but once I try to edit them it just attempts
to load the 'Workflow Editor' but it never does. How can I solve this? Do I
have to
Noa has the right idea, but if you're asking for how to split a dataset into
two non-overlapping halves you'll want to use Select First and Select Last,
instead of random lines. Get an accurate line count from your file using the
Line/Word/Character count tool and then split it right in the
This should be fixed as of yesterday afternoon. Are you still having issues?
-Dannon
On Mar 1, 2012, at 11:28 AM, Keith E. Giles wrote:
All of a sudden I can not upload any files from the FTP server. The files
upload into my ftp directory fine, but when I try to upload them into galaxy,
Greg,
The problem here is that the galaxy update failed to merge a change to run.sh
because of minor customizations it has. We'll have a long term fix out for
this soon, but for now what you can do is ssh in to your instance and update
run.sh yourself prior to restarting galaxy. All you need
There was a temporary cluster issue, but it looks like jobs are running again.
Try resubmitting your jobs now, and they should succeed.
-Dannon
On May 1, 2012, at 8:30 PM, Jeremy Coate wrote:
Hi all,
FYI, I've gotten the same error recently when trying to run Bowtie (using
Galaxy Main).
Hi,Just wanted to add a few clarifications here. It definitely *is* currently possible to transfer a workflow from one instance to another instance that does not have (some or all) of the tools for a particular workflow.The error you're running into "No JSON object" means that you likely have the
, considering me as a beginer. Thanks. Sorry for pushing this
question.
Vasu
On Fri, May 25, 2012 at 11:33 AM, Dannon Baker dannonba...@me.com wrote:
Hi,
Just wanted to add a few clarifications here. It definitely *is* currently
possible to transfer a workflow from one instance to another
My hunch is that there's a race condition during boot that I haven't had a
chance to track down and fix yet. I've actually disabled the share_string
launch parameter using Galaxy's built-in cloudlaunch until this has been fixed.
You can definitely still use the share string, but start the
Looking at your screenshot, you have Use a built-in index selected. If you
change this to Use one from the history, do you see your fasta file listed?
-Dannon
On Oct 10, 2012, at 9:02 AM, greg margeem...@gmail.com wrote:
Thanks Jen. But it looks like the datatype was already set to fasta.
They were introduced and described in this news brief (with screenshots!):
http://wiki.g2.bx.psu.edu/DevNewsBriefs/2011_05_20
Hope this helps,
Dannon
On Oct 30, 2012, at 7:33 PM, neil.burd...@csiro.au wrote:
Thanks Bjorn,
But I can't seem to locate the symbol/icon (looks like
Ahh, I see what's going on. Galaxy relies on the Input Dataset step for this
feature. If you use these in your workflow, Galaxy will be able to perform the
batch execution. Find them in the workflow editor under Workflow control -
inputs.
-Dannon
On Oct 30, 2012, at 8:46 PM,
d 3 as its not connected on the workflow diagram? Neil-Original Message-From: Dannon Baker [mailto:dannonbaker@me.com] Sent: Wednesday, 31 October 2012 10:54 AMTo: Burdett, Neil (ICT Centre, Herston - RBWH)Cc: bjoern.gruen...@pharmazie.uni-freiburg.de; galaxy-user@lists.bx.psu.eduSubject: R
- and me - could not go any further
(i.e. jobs are grey and never start to run). Class ended almost three hours
ago.
Does this help?
LTR
On 11/7/12 2:52 PM, Dannon Baker wrote:
Can you describe more about what is broken with your cloud install?
Regarding main - the server has been
wrote:
It looks like both the main server and our local install are frozen. Nothing
has run since we started yesterday at about 11:30am. Anybody know why?
LTR
On 11/7/12 4:05 PM, Dannon Baker wrote:
Main will complete the jobs eventually, though obviously that's not
particularly useful
It isn't normal, but this can happen during periods of extremely high load like
we're currently experiencing. If you leave your jobs in the queue, they'll
execute as soon as possible - don't cancel or restart your jobs as this will
only move them to the back of the queue and delay completion.
be receptive to some help, so you should mail him.
LTR
On 11/7/12 4:05 PM, Dannon Baker wrote:
Main will complete the jobs eventually, though obviously that's not
particularly useful in the context of your class today. How is your cloud
instance set up? Cloud or local instances should
That's just the section demarcation stating that everything following (until
the next such bracketed line) is a property of the 'server:main' section --
there should be no need to change that, though you can certainly change any of
the properties within the section as needed.
-Dannon
On Nov
On Dec 19, 2012, at 11:09 AM, Sun, Wenping [USA] sun_wenp...@bah.com wrote:
I also have the preconfigured cloud instance set up recently. However, when I
stopped the instances (master and cluster nodes) from aws, I couldn't get the
galaxy web running again (the instance running however the
It looks like you've worked on both the public galaxy site we provide
(main.g2.bx.psu.edu) and your own cloud instance. Data on the public instance
won't be automatically migrated to the cloud instance and vice versa.
All work done on the cloud site will remain there and persist after
] sun_wenp...@bah.com wrote:
Thanks and my question is--
How to shutting down the cloud if working on main.g2.bx.psu.edu?
Thanks,
Kathryn
-Original Message-
From: Dannon Baker [mailto:dannonba...@me.com]
Sent: Thursday, December 20, 2012 1:38 PM
To: Sun, Wenping [USA]
Cc: galaxy-u
On Dec 20, 2012, at 2:33 PM, Sun, Wenping [USA] sun_wenp...@bah.com wrote:
Thank you very much for the information.
For the last part of using ec2 instances at aws, is there an option that I
can control galaxy's operation at aws site? This way I can start/stop the
instance when I need. I
On Dec 20, 2012, at 2:52 PM, Sun, Wenping [USA] sun_wenp...@bah.com wrote:
The problem is that if use usegalaxy.org/cloudlaunch to restart galaxy, it
will launch to main.g2.bx.psu.edu, where I have no control on the data
security and running queues. Meanwhile, the correspondingly initiated
In the main (non-admin) cloudman UI you'll see a little icon next to the volume
size. Click this and you'll have the opportunity to enter a new size. Upon
submitting this, galaxy will need to temporarily shut down, but it should be
automatically restarted once the procedure is complete. Note
To be clear, your admin user still works on this instance but another one does
not? If this is the case, can you log in as the admin user (and, if not,
simply register a new user and make it an admin) and take a look at the user
list in the admin panel?
To get to the user list when in Galaxy,
On Jan 2, 2013, at 5:17 PM, Sun, Wenping [USA] sun_wenp...@bah.com wrote:
1. how to retain my previous work?
If you were logged in when you were working previously, we just have to figure
out who you were logged in as, and log back in. You may also want to check
Saved Histories to make sure
Geert, this is great stuff!
One small correction -- the API is enabled by default as of revision
7022:8376ad08ae41 (April 2012).
-Dannon
On Jan 16, 2013, at 1:17 AM, Geert Vandeweyer geertvandewe...@gmail.com wrote:
Hi,
I've put together some exempels for activating and using the api.
Hey Mark,
Yep, sure can. Just click on the gear in the history panel and go to Copy
Datasets, and copy those datasets you're interested in to th specific new
history you want to use.
-Dannon
On Feb 1, 2013, at 10:15 AM, mark.r...@syngenta.com wrote:
Hi All
Let’s say that I have results
Dikla,
After refreshing the browser, the most up-to-date view of the history should
definitely be available. Are you positive you're looking at the same history
in both places? I would verify that there's nothing in Saved Histories that
looks like what you're expecting.
-Dannon
On Feb 13,
Hi Tomaž,
The script depends on galaxy libraries, but could probably be set up
standalone if you made the appropriate libraries available -- the source is
distributed with galaxy, see
https://bitbucket.org/galaxy/galaxy-central/src/tip/tools/fastq/fastq_trimmer_by_quality.py?at=default
-Dannon
Actually, you can do this in workflows out of the box in Galaxy (as long as
your instance is configured to send mail).
All you need to do is edit the workflow, select the step you want to be
notified following, and add a Step Action- Email Notification.
On Fri, May 17, 2013 at 9:41 AM, Geert
Hi Alejandro,
It should show up if you search for the AMI ID, which is ami-da58aab3.
That said, the easiest way to launch a galaxy cloud cluster if you're not
already familiar with EC2 is probably using usegalaxy.org/cloudlaunch.
This interface will guide you through the launch process without
Hi Ann,
My guess is that this is related to the issue you were having before. I'm
taking a look now.
-Dannon
On Mon, Jun 10, 2013 at 7:31 PM, Ann Holtz-Morris, M.S.
aholtzmor...@chori.org wrote:
Hi,
I’m trying to create a new custom build . I keep getting *GURU
MEDITATION:
Hi Jun,
Thanks for the clarification. Workflow step annotations would best suit
your needs, I think. When you're in the editor, click on any step and on
the right side you'll see a field Annotation / Notes which will be
displayed when the workflow is viewed. This can be used to clear up any
On Sun, Aug 25, 2013 at 3:35 PM, Deniz Erezyilmaz deniz...@gmail.comwrote:
When I try to add nodes from the galaxy console, they never register as
available and the icons never switch from blue to yellow to green. The
cluster status log shows that they have been added. However, when I try to
Do you have debug enabled in your universe_wsgi.ini? IIRC, this causes the
entire request to be loaded into memory (which is a bad thing when the
response is 20GB).
On Thu, Aug 29, 2013 at 3:50 PM, Delong, Zhou delong.z...@usherbrooke.cawrote:
Hello,
I wanted to download the accepted
Sorry for not being able to take a look at this sooner, thanks for figuring
it out and posting back! This one must have fallen through the cracks when
we updated all the paths with the last Cloudman release, I'll make a note
to fix it with our next minor update.
-Dannon
On Thu, Sep 26, 2013 at
Hi PT,
What exactly do you mean by Galaxy on the Cloud appears to expect that the
imported and converted fastq files are in the same S3 bucket where the
fastq.gz files were? Once imported from S3, you're correct in that
everything will be on the local EBS volume.
-Dannon
On Sun, Oct 6, 2013
That means that the galaxy instance for your cluster didn't start. It
probably should have. Can you send me (directly, without the list -- it
can contain sensitive info) the cloudman log from the admin panel?
-Dannon
On Tue, Oct 8, 2013 at 9:17 AM, Yan He yanh...@hotmail.com wrote:
Dear
Can you send me the more detailed full cloudman log from the admin
interface (it may be quite large). This will help me see what may have
happened.
On Wed, Oct 9, 2013 at 3:56 PM, Lei Yan leiyan2...@gmail.com wrote:
Hi all,
I found some very strange problems on our cloud Galaxy (
and Translational Genomics
The University of Tennessee Health Science Center
On Wed, Oct 9, 2013 at 4:04 PM, Dannon Baker dannon.ba...@gmail.comwrote:
Can you send me the more detailed full cloudman log from the admin
interface (it may be quite large). This will help me see what may have
happened
Hey Francis,
There's a bug in the current release of cloudman that causes files fetched by
galaxy (this doesn't affect direct http or ftp upload) to use the root volume
as temporary storage, which has very little space. This is fixed in the next
release scheduled to coincide with the
The right approach here is probably to use history tags (at the top of a
history panel, click the tag icon just below the history name). You could
tag several histories with a particular sample name, organism, etc. While
you can *search* for histories by tags and get a list of, say, all Mouse
Sébastien,
This seems to be a galaxy bug from a little while back. To fix your cloud
instance, go to the cloud admin console and click Update Galaxy, and the
problem should be resolved once galaxy updates and restarts.
-Dannon
On Fri, Jan 3, 2014 at 6:42 PM, Sébastien Vigneau
After adding yourself as an admin in Cloudman, your galaxy instance
restarted, correct? If so, can you double check that the cloudman admin
interface indicates your exact email address that you've logged into galaxy
as?
-Dannon
On Mon, Feb 3, 2014 at 12:32 PM, Malik, Shivani
Hey Eric,
Looking into this. Can you send the exact error/trace if available?
-Dannon
On Thu, May 22, 2014 at 10:17 AM, Paniagua, Eric epani...@cshl.edu wrote:
Hi,
I am running a Galaxy instance at Cold Spring Harbor Laboratory, and in
the process of preparing an update I have
-user-boun...@lists.bx.psu.edu [
galaxy-user-boun...@lists.bx.psu.edu] on behalf of Paniagua, Eric [
epani...@cshl.edu]
Sent: Thursday, May 22, 2014 1:38 PM
To: Dannon Baker
Cc: Galaxy [galaxy-u...@bx.psu.edu]
Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
Hi
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