Bumping this questionno response in over a week...
Hi all - I've recently come back to Galaxy to see how its progressed over
the last few years. The tools shed is completely new to me and will take
some exploring on my part.
My immediate question is if there is a way to import a large
Let me see if I can find what I need and if I need any help, I'll let you
know. Thanks!
On Thu, Nov 13, 2014 at 12:14 PM, Dannon Baker dannon.ba...@gmail.com
wrote:
Hey Ryan,
Sorry this fell through the cracks. A script to import large sets of
files to data libraries, for example, would
://myhost:myport/api/libraries?key=my_key
I get a JSON response with the libraries I've already added. Something
must be wrong at the script level?
On Thu, Nov 13, 2014 at 12:50 PM, Ryan G ngsbioinformat...@gmail.com
wrote:
Let me see if I can find what I need and if I need any help, I'll let you
I'm following the guide on
https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial to
add a tool from the tool shed.
The tutorial uses 'bwa_base', but I don't see that. So instead, I'm using
'bwa_mem'. I choose 'Preview and Install', then 'Install to Galaxy'. I
then select to
sheet (txt) file? I have a
text file with 3 columns: sample name, location of fastq files.
I haven't seen a way to import this and haven't seen anything in the docs
either. I suspect the answer is no, but I'm hoping the answer is actually
yes?
Ryan
the same error).
Thanks,
Ryan
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will not be read. In this
instance, you should set $PATH in the startup file or use.
Thanks!
Ryan
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/UCSC/mm10/Sequence/sam/
mm10.fa$
Even with the correct file, I still get the same error in the paster.log.
Does this get saved in the database? How do I resolve this?
Thanks for the help!
Ryan
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https://main.g2.bx.psu.edu/history/export_archive?id=e0b0f57abd62f2aa -O
F:\Galaxy\Ryan\rnd003bucknell.edu\Cattle_seq.galaxy
However, we seem to be getting an error on all files from all of their accounts
and no files are being saved. See below for cmd prompt output.
Resolving main.g2
I am trying to view html results from the SeqPos Tool on Galaxy/Cistrome Main,
but keep receiving Please use a frames compatible browser when viewing this
output message. I have tried this in Google Chrome, IE9, and Firefox but
receive the same message in all three browsers.
I'm able to connect. It could be a firewall issue form your institution.
I know mine doesn't allow any FTP in or out.
On Tue, Aug 14, 2012 at 12:10 PM, suzan katie suz.ka...@gmail.com wrote:
Hello everyone,
I am trying to upload files (size:6GB) via ftp and i am using FileZilla
for ftp
My two cents---
$5K won't buy everything you need, but it will get you started. I think at
least a 4-core machine with 16GB of RAM should be sufficient for most jobs.
If you know you need more, get more RAM.
Galaxy is a hog on disk space, so try to maximize disk space. I would set
up 2 small
Agreed. User driven is good. Having developer(s) available to answer
questions would be helpful...that's what I was alluding to...
On Sun, Apr 29, 2012 at 10:37 PM, Dave Clements
cleme...@galaxyproject.orgwrote:
Hi Ryan, Ann, and everyone else
I second what Nate says (I always do :-). I
One question - Are the Galaxy developers involved in this or is this for
user's only? It may be helpful to have developers on the call to provide
information that users do not necessarily have.
On Fri, Apr 27, 2012 at 8:21 PM, steve.mcma...@csiro.au wrote:
Sounds like a good idea to me. I'm
This is a great idea.
On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein
annbl...@eng.uiowa.edu wrote:
Hi everyone -
Here at the University of Iowa we are working on deploying Galaxy locally
for campus wide access. I am interested in forming a community of other
institutions trying to
scheduler. Thanks
for pointing out details in the code Nate.
--
Shantanu.
On Jan 20, 2012, at 9:35 AM, Nate Coraor wrote:
On Jan 18, 2012, at 11:54 AM, Ryan Golhar wrote:
Nate - Is there a specific place in the Galaxy code that forks the
samtools index on bam files on the cluster
'qstat -f | grep jobname' will give you the full jobname without
truncation. Personally, I think the qstat reporting gives too little
information. I've written a perl script to parse the output of qstat -f to
give a bit more information. So truncation of jobnames for qstat shouldn't
be an
I'm using Galaxy on a ROCKS cluster. I installed Galaxy on the headnode.
I'm using PBS instead of SGE though. It shouldn't make a difference.
I haven't thought about deploying Galaxy as a Roll if that's what you are
referring to. Only because Galaxy doesn't need to run on all the nodes, it
Nate - Is there a specific place in the Galaxy code that forks the samtools
index on bam files on the cluster or the head node? I really need to track
this down.
On Fri, Jan 13, 2012 at 12:54 PM, Ryan Golhar
ngsbioinformat...@gmail.comwrote:
I re-uploaded 3 BAM files using the Upload system
So I just tried restarting Galaxy and it downloaded a bunch of new eggs
then errored out. My run.sh script didn't change so how do I start Galaxy
now???
[galaxy@bic galaxy-dist]$ ./run.sh --start-daemon
Some eggs are out of date, attempting to fetch...
Fetched
ah yes. Thanks.
On Tue, Jan 17, 2012 at 12:30 PM, Dannon Baker dannonba...@me.com wrote:
That should be ./run.sh --daemon, not --start-daemon. The error is just
that --start-daemon is an unknown option.
-Dannon
On Jan 17, 2012, at 9:25 AM, Ryan Golhar wrote:
So I just tried
I re-uploaded 3 BAM files using the Upload system filepaths
On Fri, Jan 13, 2012 at 10:53 AM, Nate Coraor n...@bx.psu.edu wrote:
On Jan 12, 2012, at 11:41 PM, Ryan Golhar wrote:
Any ideas as to how to fix this? We are interested in using Galaxy to
host all our NGS data. If indexing
samtools? Maybe I can add a check of
some sort to see what's going on?
On Fri, Jan 13, 2012 at 10:53 AM, Nate Coraor n...@bx.psu.edu wrote:
On Jan 12, 2012, at 11:41 PM, Ryan Golhar wrote:
Any ideas as to how to fix this? We are interested in using Galaxy to
host all our NGS data. If indexing
file for MarkDups?
Ryan
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annbl...@eng.uiowa.edu wrote:
Hi Ryan -
I have done similar things with our tools as well. For now I have edited
the xml file to include the following option in the command section that
would get passed into the picard script wrapper:
--maxjheap=8g
I considered exposing this out in the UI
Any ideas as to how to fix this? We are interested in using Galaxy to host
all our NGS data. If indexing on the head node is going to happen, then
this is going to be an extremely slow process.
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it is also set to True:
[galaxy@bic galaxy-dist]$ grep Ryan *.log
runner0.log:galaxy.jobs WARNING 2012-01-10 22:17:26,381 Ryan Golhar -
self.set_metadata_externally = True
Clearly something else is going on here. On my last import of BAM file,
even after samtools finished indexing
On Wed, Jan 11, 2012 at 11:16 AM, Nate Coraor n...@bx.psu.edu wrote:
On Jan 11, 2012, at 10:56 AM, Ryan Golhar wrote:
it is also set to True:
[galaxy@bic galaxy-dist]$ grep Ryan *.log
runner0.log:galaxy.jobs WARNING 2012-01-10 22:17:26,381 Ryan Golhar -
self.set_metadata_externally
I thought I once saw a publication (or presentation maybe) talking about
AnnoVar being available in Galaxy but I don't see it online or in
galaxy-dist, nor in the tool shed. Is it really available?
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PM, Ross ross.laza...@gmail.com wrote:
Hi Ryan,
Yes, the Picard tool mandates a bizarre bait/target format file for
reasons which might best be addressed to the Picard devs - they may
have some very good reasons although I can't imagine what they are.
:)
Yes, automated conversion of any
, 2012 at 11:24 AM, Ryan Golhar
ngsbioinformat...@gmail.comwrote:
In case anyone is interested I posted a message to samtools-dev and got a
few responses about it. The thread is called 'Picard bait/target format
file for HsMetrics'. Now, for Galaxy, I think the wrapper should not
accept
On Tue, Jan 10, 2012 at 11:43 AM, Ryan Golhar
ngsbioinformat...@gmail.comwrote:
Hi Ryan,
You could check it in lib/galaxy/config.py, after it's read. By any
chance, are you using galaxy-central vs. galaxy-dist? It's possible that
due to a bug I recently fixed and a certain combination
On Fri, Jan 6, 2012 at 12:55 PM, Ryan Golhar ngsbioinformat...@gmail.comwrote:
This indicates that set_meta is running locally, in the runner process.
Can you make sure there's not a typo in your config? The other
possibility is that external metadata setting failed and it's being retried
Hi all - I think there is a problem with the Picard HSMetrics wrapper in
Galaxy. The wrapper accepts a BAM files and a BED file. However the BED
file isn't really in a BED format...it requires a SAM header before the BED
lines. This really isn't a BED file format. I'm not quite sure how Galaxy
Derrick,
Take a look at the section entitled Job runner URL on
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster. But as I
understand it, you don't need to do anything since the drmaa library is
part of your SGE installation. Just make the node Galaxy runs on an exec
host.
Ryan
Whoops. That's what I mean...a submission host, not an exec host.
On Mon, Jan 9, 2012 at 11:13 PM, Derrick LIN klin...@gmail.com wrote:
Thanks Ryan,
I have been following that guide. I can configure the galaxy host to be an
exec host, although it makes more sense to be a submission host
This indicates that set_meta is running locally, in the runner process.
Can you make sure there's not a typo in your config? The other
possibility is that external metadata setting failed and it's being retried
internally (if that was true, you'd see messages indicated such in the
server
On Jan 4, 2012, at 6:44 PM, Ryan Golhar wrote:
On Wed, Jan 4, 2012 at 5:17 PM, Ryan Golhar ngsbioinformat...@gmail.com
wrote:
I'm adding Data Libraries to my local galaxy instance. I'm doing this
by importing directories that contain bam and bai files. I see the bam/bai
files get added
I set it to run on the cluster:
[galaxy@bic galaxy-dist]$ grep upload1 universe_wsgi.runner.ini
#upload1 = local:///
On Thu, Jan 5, 2012 at 11:33 AM, Nate Coraor n...@bx.psu.edu wrote:
On Jan 5, 2012, at 11:29 AM, Ryan Golhar wrote:
On Jan 4, 2012, at 6:44 PM, Ryan Golhar wrote
On Jan 5, 2012, at 11:46 AM, Ryan Golhar wrote:
I have three bam files that I'm trying to merge. The job runs for a bit
then errors saying there is a problem. When I look at runner0.log I see:
galaxy.jobs.runners.pbs DEBUG 2012-01-05 00:12:50,193 (19) submitting
file /home/galaxy
I discovered the problem. My pbs queue has a wall time restriction of
3600 seconds.
Is there a way to configure Galaxy to keep the job files for only failed
jobs? I'd like to keep these two settings on, but find it unnecessary if
jobs successfully complete.
The other option I would
I haven't found a way to fix the status on BAM files being imported. They
still read Job still running. So I thought I'd just delete the whole
data library and start a new. From the Admin page, I click Manage Data
Libraries, then select all the data libraries by clicking the checkbox next
to
far) and allows initial requests with and
without the trailing backslash. Can I recommend this as a change to the
docs? Also, can I recommend documenting a separate galaxy.conf for Apache?
I'd be happy to provide mine as a model, if you'd like.
Ryan
be beneficial to invoke pipelines from the command
line instead of being forced to use the web-based interface. command line
is beneficial for large #'s of datasets that need to be analyzed.
Ryan
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I have a cluster (cluster A) set up with Galaxy. Our sequencing data gets
mapped to hg19, then the resulting BAM files are placed on a SAN connected
to a different cluster (cluster B) that cluster A does not have NFS access
to. We cannot install an FTP server on cluster B either. The only way
I'm adding Data Libraries to my local galaxy instance. I'm doing this by
importing directories that contain bam and bai files. I see the bam/bai
files get added on the admin page and the Message is This job is running.
qstat shows the job run and complete. I checked my runner0.log and it
On Wed, Jan 4, 2012 at 5:17 PM, Ryan Golhar ngsbioinformat...@gmail.comwrote:
I'm adding Data Libraries to my local galaxy instance. I'm doing this by
importing directories that contain bam and bai files. I see the bam/bai
files get added on the admin page and the Message is This job
On Wed, Jan 4, 2012 at 5:17 PM, Ryan Golhar
ngsbioinformat...@gmail.comwrote:
I'm adding Data Libraries to my local galaxy instance. I'm doing this by
importing directories that contain bam and bai files. I see the bam/bai
files get added on the admin page and the Message is This job
I set up my Apache server to act as a proxy server based on the docs at
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
My pages aren't loading correctly and I discovered that since I have galaxy
installed as its own user, the apache user account does not have access to
the galaxy files. I
Hi all - I'm setting up Galaxy under Apache and following the guide for a
production environment. I've got the proxy server running properly and am
now setting up load balancing. I currently start galaxy (for testing)
using 'sh run.sh --reload' so I can stop galaxy using Ctrl-C.
I'm following
Hi all - I had this problem once before with a previous installation, and
thought it was fixed, but I'm seeing it again and not sure its related.
I have Galaxy running with a Proxy server on apache to get /galaxy instead
of using port 8080. I've disabled load balancing and running everything in
On Tue, Jan 3, 2012 at 4:21 PM, Ryan ngsbioinformat...@gmail.com wrote:
Hi all - I had this problem once before with a previous installation, and
thought it was fixed, but I'm seeing it again and not sure its related.
I have Galaxy running with a Proxy server on apache to get /galaxy instead
On Tue, Jan 3, 2012 at 4:21 PM, Ryan ngsbioinformat...@gmail.com wrote:
Hi all - I had this problem once before with a previous installation, and
thought it was fixed, but I'm seeing it again and not sure its related.
I have Galaxy running with a Proxy server on apache to get /galaxy
Thank you Marco and Hans for your solutions. I installed the R-devel and it
fixed the issues. I now have R 2.12.2 and rpy 1.0.3 running smoothly.
Thanks!
From: Marco Moretto [mailto:marco.more...@gmail.com]
Sent: Tuesday, June 21, 2011 11:49 PM
To: Ryan Davis
Cc: galaxy-dev@lists.bx.psu.edu
this step:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64/R/lib/
However I get the following error with the install of rpy 1.0.3.
Thanks for the help,
Ryan
[cgtepper@hobbes rpy-1.0.3]$ python setup.py install
RHOMES= []
DEBUG= True
Setting RHOMES to ['/usr/lib64/R']
### Using R verion 2.12.2
This is Safari on Mac OS X. I just reverted to my backup and the
problem still exists so I don't know what is going on now.
On 4/11/11 2:35 PM, Peter Cock wrote:
On Mon, Apr 11, 2011 at 7:26 PM, Ryan Golhargolha...@umdnj.edu wrote:
I just updated my local galaxy instance using hg pull
Yeah, I pulled down a new version of galaxy-dist to a new directory and
am comparing the differences using diff on my current instance. For
some reason hg pull -u didn't work. It aborted because I installed a
bam.xml for igv in display_applications/igv. Apparently one was added
to
I screwed Galaxy. I will delete / reinstall it. At least I will delete
it. I think I will revert back to the shell for awhile to get some work
done. I've spent *way* too much time trying to get galaxy to work
properly. Thanks for all the help everyone.
On 4/11/11 4:32 PM, Ryan Golhar
-rw-r--r-- 1 gordon hannon 35 Apr 7 00:57 1.sam
So in short, this whole sam-to-bam wrapper tool is not suitable for
large SAM files (if they don't fit entirely in memory), and not for
error checking of invalid SAM files.
-gordon
On 04/07/2011 12:30 AM, Ryan Golhar wrote:
Here's what I
empty'
except Exception, e:
It only exists in galaxy-central, not in galaxy-dist which is what you
recommend people to use.
Both me and Ryan have this line of code, and I'm sure we've both pulled since
April 2010.
It's really just intended to catch weird errors that don't throw an
actual
extracting alignments from
(/home/galaxy/galaxy-dist/database/files/000/dataset_785.dat),
However running the samtools command works fine
On 4/5/11 5:58 PM, Ryan Golhar wrote:
I've performed an alignment using BWA on a file of paired-end illumina
reads. The SAM file looks fine, and contains header
So it looks like I can get small sam files converted to bam files, but
not large sam files (~50GB-80GB). I'm still trying to debug this, but
not sure what's going on.
Has anyone else run into anything like this?
On 4/6/11 10:08 AM, Ryan Golhar wrote:
Any ideas why I would get this? If I
is this failing in one case and not the other? I'm stuck. Help
Ryan
On 4/6/11 4:58 PM, Ryan Golhar wrote:
So it looks like I can get small sam files converted to bam files, but
not large sam files (~50GB-80GB). I'm still trying to debug this, but
not sure what's going on.
Has anyone else run
for losing
disk space from SAM files unnecessarily.
Ryan
On 4/5/11 1:18 PM, Assaf Gordon wrote:
Hello Ryan,
I'm in the exact same situation with my bowtie/tophat tools,
going back and forth between outputing a SAM, sorted SAM, BAM or sorted BAM,
and I'm still not sure what's the best method
I do?
Ryan
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Note about multithreaded bowtie:
currently the tools use 10 threads (hard-coded in the XML files) - easily
changeable.
If possible, have the user indicate as a parameter how many threads they
wish to use.
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used the instructions shown on this bitbucket wiki
(eg hg clone https://[your id]@bitbucket.org/galaxy/galaxy-central/ )...
I think it would be better if step 1 was in sync with step 5.
How can I resolve the fact that I used Step 1 initially and now want to
update my instance of Galaxy?
Ryan
Nevermind, I spoke to soon. I see some on the Wiki.
On 3/21/11 2:11 PM, Ryan Golhar wrote:
Are there any automated functional and/or acceptance tests that can be
run on a locally installed Galaxy instance?
I recently installed Galaxy here. A few people in our group have
encountered problems
in the public version of galaxy?
Ryan,
We compile Cufflinks ourselves as well for main, but for some reason we don't
see the message that you're seeing when Cufflinks is run. We have Cufflinks
v0.9.3, but I wonder whether we might be using a slightly older version of the
code. In any case, looking
Hi all - I'm running Galaxy on my Redhat linux cluster. When I run
cufflinks from the shell I get the error/warning:
cufflinks: /usr/lib64/libz.so.1: no version information available
(required by cufflinks)
but it still seems to run ok. It looks like Galaxy is choking on this.
I tried
Does anyone have an updated tool-runner .XML and .py for MACS 1.4? It
looks like Galaxy uses an older version of MACS.
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Is there a way to quickly determine what fastq filetype a particular
fastq file is? I ask because I was recently given a fastq which which I
incorrectly assumed to be fastqsanger. When I ran a fastx tool on the
file, the tool seg faulted. It took me a while to figure out that the
fastq type
I've configured my local instance of galaxy to run with drmaa.
Unfortunately, there is a problem that after some time, galaxy loses its
ability to talk to Torque, hence Galaxy thinks long-running jobs have
failed and its unable to submit new jobs.
I have no idea how this stuff works
Ryan, congratulations on getting this far!
Thank you! :)
Ok, so I think I have everything set up correctly. I'll test my
cluster integration tomorrow. For now, I can see galaxy from my web
browser.
First issue - When I go to User - Login and try to log myself in
(I've
the shell, the job runs, but when the
web interface submits the job it doesn't. In both cases, its the galaxy
user account so I don't think environment variables are to blame.
On 2/18/11 10:26 AM, Ryan Golhar wrote:
Ryan, congratulations on getting this far!
Thank you! :)
Ok, so I think I have
I'm setting up Galaxy to run on my cluster using drmaa. I can see jobs
getting submitted to Torque however the jobs keep failing, because the
tools are in the default system path.
How do I tell galaxy to append a directory to the path used by jobs?
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Ryan Golhar wrote:
I'm setting up Galaxy to run on my cluster using drmaa. I can see
jobs getting submitted to Torque however the jobs keep failing,
because the tools are in the default system path.
How do I tell galaxy to append a directory to the path used by jobs?
Hi Ryan,
Whatever
Ryan Golhar wrote:
Ryan Golhar wrote:
I'm setting up Galaxy to run on my cluster using drmaa. I can see
jobs getting submitted to Torque however the jobs keep failing,
because the tools are in the default system path.
How do I tell galaxy to append a directory to the path
On 2/18/11 2:37 PM, Glen Beane wrote:
On Feb 18, 2011, at 2:12 PM, Ryan Golhar wrote:
It turns out the user's environment is not set up for batch jobs,
only the system environment. I too added . ~/.bashrc to
lib/galaxy/jobs/runners/drmaa.py.
I'm afraid this is a kludgy fix that will break
Hi all - I'm uploading datasets into my local instance by importing from
the filesystem w/o copying into Galaxy.
Importing of uncompressed files works properly. The files I'm importing
are owned by user1 and a read-able by everyone, including the galaxy
user. The galaxy user does not have
I've set up a local instance of Galaxy following the instructions in the
wiki for a production instance. I'm running on CentOS with Apache, and
a mysql database server.
Everything looks great when viewed directly through the Galaxy web
server on port 8080.
I've implemented the Serving
SOLVED. I copied/paste the Rewrite rules for apache from the wiki
without updating the paths to my installation...once I did that, all
worked well.
On 2/17/11 5:07 PM, Ryan Golhar wrote:
I've set up a local instance of Galaxy following the instructions in
the wiki for a production
Nevermind (once again). I figured out I need to compile it from the
torque...
On 2/17/11 10:30 PM, Ryan Golhar wrote:
I'm configuring my local install of galaxy to work with my torque/maui
cluster. On the Config/Cluster wiki page, there is mention about telling
Galaxy where the DRMAA library
I'm configuring my local install of galaxy to work with my torque/maui
cluster. On the Config/Cluster wiki page, there is mention about
telling Galaxy where the DRMAA library is located. The example given
points to libdrmaa.so.
I've searched my torque installation and haven't come across
Ok, so I think I have everything set up correctly. I'll test my cluster
integration tomorrow. For now, I can see galaxy from my web browser.
First issue - When I go to User - Login and try to log myself in (I've
already registered myself), it looks like it works, but the browser get
Hi - I'm running CentOS 5.5. My version of python is:
[root@genomes ~]# which python
/usr/bin/python
[root@genomes ~]# python -V
Python 2.4.3
I just downloaded galaxy to run a local instance using:
hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist
and then tried to run it using 'sh
/ibmfcarray/galaxy_dist/lib/galaxy/eggs/scramble.py, line
243, in scramble
raise last_exc # only 1 failure out of the crate, be more informative
galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build
failed for python_daemon 1.5.5
On 2/16/11 12:58 AM, Ryan Golhar wrote:
Hi
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