I'm trying to translate this command line run into the Galaxy GUI but
I'm not seeing a place to specify the .gtf file.
Does anyone know?
tophat2 -p 8 -G /groups/bowtie2_index/mRNA.gtf -o /groups/hp_1
/groups/genome /groups/reads.fastq
thanks,
Greg
That's very helpful! Thanks.
-Greg
On Tue, Dec 18, 2012 at 11:39 AM, Jennifer Jackson j...@bx.psu.edu wrote:
Hello Greg,
Open up TopHat settings to use: to Full Parameter list to find the
option: Use Own Junctions: and set this to Yes. There will be a new
option underneath it for Use Gene
Hello Joachim,
Thanks for reporting this. This issue was resolved a couple of weeks ago, but
did not make it into the cutoff for the last Galaxy distribution release. It
is corrected on the test Galaxy tool shed and will be included in the next
Galaxy release.
Greg Von Kuster
On Dec 12
been done automatically
for you when you installed the repository, but I'm not sure why it didn't.
Maybe you're running an older version of Galaxy that doesn't include this
automated feature.
Greg Von Kuster
!-- Locations of all bismark converted bs-seq references --
table name
I see this setting at the top of universe_wsgi.ini:
# Configuration of the internal HTTP server.
[server:main]
I'm confused what that's for. Do I need to change it?
Thanks,
Greg
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-- 1 galaxy scicomp 20K Nov 16 08:54 tmptzuSYJ
-rw-r--r-- 1 galaxy scicomp 20K Nov 15 15:47 tmpu77PEK
-rw--- 1 galaxy scicomp 286 Nov 16 08:58 tmpykoBIq
-rw--- 1 galaxy scicomp 134M Nov 16 08:58 upload_file_data_G3eZEg
Thanks,
Greg
On Fri, Nov 16, 2012 at 10:00 AM, Nate Coraor n...@bx.psu.edu wrote:
On Nov 16, 2012, at 9:14 AM, greg wrote:
Are you running the upload tool on a cluster?
--nate
Well I have Galaxy set up to send it's jobs to SGE/qsub but I haven't
verified that it's doing that yet. I wanted to upload
Also what would I look for in the log file to know if it's issuing jobs?
I started a new upload, but I don't see anything from the galaxy user
when I run qstat.
Thanks again.
Greg
On Fri, Nov 16, 2012 at 12:22 PM, greg margeem...@gmail.com wrote:
I guess I'm still confused about new_file_path
be going wrong there?
-Greg
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available to your users.
Rolling back an installed tool shed repository within a Galaxy installation has
never been supported - instead just uninstall.
Greg Von Kuster
On Nov 14, 2012, at 11:06 AM, Paul-Michael Agapow wrote:
Just today, we had a case where we wanted to rollback to a previous version
the virtual env on the python path in
the log file so I think it's working.
Now I'm on to a database connection problem. Thanks for the help!
-Greg
On Fri, Nov 9, 2012 at 3:09 PM, Scott McManus scottmcma...@gatech.edu wrote:
Whoops. I missed that (obviously).
When you use su, you preserve
my first question is why does it appear to be using Python 2.6? Is
it not using my virtual env? Am I using virtual env incorrectly?
Thanks,
Greg
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Thanks, but I'm confused. How will the cluster jobs galaxy submits
know to use the virtual env?
Or since all jobs are submitted as the galaxy user it will have the correct one?
-Greg
On Tue, Nov 6, 2012 at 3:12 PM, Carlos Borroto carlos.borr...@gmail.com wrote:
On Tue, Nov 6, 2012 at 2:27 PM
directory within galaxy-dist.
Thanks,
Greg
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Thanks Scott. I did turn up: /sge/8.0.1p4/lib/lx-amd64/libdrmaa.so.1.0
I guess that would be it.
For a followup question ,how do I make the DRMAA_LIBRARY_PATH variable
permanent on the machine?
-Greg
On Mon, Nov 5, 2012 at 3:03 PM, Scott McManus scottmcma...@gatech.eduwrote:
I forgot
And am I correct in the thinking that only the machine hosting the
galaxy web interface and submitting jobs needs the export
DRMAA_LIBRARY_PATH= variable?
The normal nodes running jobs don't need this, right?
Thanks,
-Greg
On Mon, Nov 5, 2012 at 3:12 PM, greg margeem...@gmail.com wrote
Well, I want it to ultimately run under Apache. Does it still make
sense to go in an init script?
thanks again,
Greg
On Mon, Nov 5, 2012 at 3:23 PM, Nate Coraor n...@bx.psu.edu wrote:
On Nov 5, 2012, at 3:15 PM, greg wrote:
And am I correct in the thinking that only the machine hosting
Thanks Jen. But it looks like the datatype was already set to fasta.
I tried setting it again and saving but it didn't seem to help.
Is there anything else I can try?
thanks,
Greg
On Tue, Oct 9, 2012 at 9:10 PM, Jennifer Jackson j...@bx.psu.edu wrote:
Hi Greg,
Nice pic, it helps! My guess
Yes that was it! I knew I was missing something obvious.
Thanks,
Greg
On Wed, Oct 10, 2012 at 9:06 AM, Dannon Baker dannonba...@me.com wrote:
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
to make sure they're contained in the
galaxy-dist directory and make sure Galaxy and all of the jobs know to
find these tools there?
Thanks,
Greg
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On Tue, Oct 2, 2012 at 2:15 PM, Nate Coraor n...@bx.psu.edu wrote:
On Oct 2, 2012, at 12:45 PM, greg wrote:
Hi guys,
I'm following the instructions here to install Galaxy on our SGE cluster.
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster
(I'm aiming for the unified install
Hello Joel,
The main Galaxy tool shed is back up - thanks for reporting this problem.
Greg Von Kuster
On Sep 30, 2012, at 5:34 PM, Joel Rosenberg wrote:
It looks like the galaxy toolshed is down.
The migration script is trying to download this:
http://toolshed.g2.bx.psu.edu/repository
configuration dialog is still appearing.
I ran the same thing yesterday with an older share string and
everything worked fine.
Any ideas what could be going on? I'm pretty stuck.
Thanks,
Greg
This is all I see in the cluster status log (I entered my share string
again on the dialog, the disk
Thanks Dannon.
I'm actually writing some documentation that I won't be able to update
again for a few months.
Will the old method (entering the share string on the initial
configuration dialog) be around for a while?
If so I'll just tell users to do that.
Thanks,
Greg
On Tue, Sep 18, 2012
a bunch!
-Greg
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Hello Fabien,
I don't understand the issue - can you provide a sample tool config that
includes these hard-coded paths? This initially sounds like an issue with the
tool configs, not the tool shed, but I may see the problem with your
clarification.
Thanks,
Greg Von Kuster
On Jul 3, 2012
that are properly defined in the tool config file
within the requirements tag set. These new tool shed features will soon be
documented in the tool shed wiki.
Thanks,
Greg Von Kuster
On Jul 3, 2012, at 12:27 PM, Fabien Mareuil wrote:
Hi,
Thank for your answer, I copy you a part of the shell
Hi Greg,
Upload your files to a Galaxy data library using a combination of Upload files
from filesystem paths without copying data into Galaxy's default data store.
See the following wiki for all the details:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
For all
Hi Greg,
Even though you are not copying the data into Galaxy's default data store,
Galaxy determines and stores certain metadata for each of the data files to
which you are linking. One of the types of metadata defined for the Bam
datatypes is it's index, which is created by a call
to the file (no copying). After at
least an hour of working, I get the error message Unable to finish
job,
tool error. Any thoughts as to how I can fix this? Thanks.
Greg
On 4/23/12, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Greg,
Even though you are not copying the data into Galaxy's
in the
tool_sheds_conf.xml file in the Galaxy install directory. For your local shed,
you'll simply need to an entry like this:
tool_shed name=Bx tool shed url=http://gvk.bx.psu.edu:9009//
p
Paul Agapow (paul-michael.aga...@hpa.org.uk)
Bioinformatics, Health Protection Agency
Thanks,
Greg
On Apr 3, 2012, at 6:07 AM, Peter Cock wrote:
On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster g...@bx.psu.edu wrote:
On Mar 24, 2012, at 7:30 AM, Peter Cock wrote:
Have you seen the README file that comes with the
Blast2GO wrapper? Perhaps the 'install from toolshed'
could be tweaked
. You need to purge all the cache in your browswer totally,
eg. in Chrome it's Preferences / Delete All Browser Data (or something
like that, I'm away from my normal computer). Just forcing a refresah with
the usual refresh/reload icon isn't enough.
Greg E
On Wed, Mar 7, 2012 at 6:52 PM, huayan gao
seen it yet -
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Library%20Security. Hopefully
it will clarify why you're seeing this. If not, you'll have to let me know the
permissions at all levels of your library in order for me to be able to help.
Thanks,
Greg Von Kuster
On Mar 10
types of
instance, (tiny/small/medium/large). Is that a recommended AMI now ? It
would be good to have a new updated AMI.
[image: Inline image 1]
Thanks !
--
Greg Edwards,
Port Jackson Bioinformatics
gedwar...@gmail.com
snap1.png___
hurdles. AWS thinks your'e a spammer and
blocks emails after a while ! but you can submit a request to get around
that.
If anyone's interested let me know.
Cheers,
Greg E
--
Greg Edwards,
Port Jackson Bioinformatics
gedwar...@gmail.com
/Admin/Config/Performance/Production%20Server
http://wiki.g2.bx.psu.edu/Admin/Config
Hopefully this helps,
Jen
Galaxy team
On 2/28/12 2:59 PM, Alejandra Rougon wrote:
Thank you Greg, I saw the wiki but I do not see the admin link in my
galaxy interface. How do you open galaxy
No, you'll need to stop and restart your Galaxy server.
On Mar 1, 2012, at 2:01 PM, Alejandra Rougon wrote:
I did close the web browser and opened it again
was that enough?
From: Greg Von Kuster g...@bx.psu.edu
To: Alejandra Rougon alerou...@yahoo.com
Cc: Jennifer Jackson j...@bx.psu.edu
on Galaxy data libraries, see this wiki:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries
Greg Von Kuster
On Feb 28, 2012, at 2:54 PM, Alejandra Rougon wrote:
Hello, I tried to search in the forums and although this question has
appeared many times I still don't have a solution.
I
numbers
(e.g., 89 - 90, 90 - 91, etc). Your migrate_versions.version database table
column has a value of 90, but your ~/lib/galaxy/model/migrate/versions
sub-directory has scripts only up to 0079... (or so it seems). Not sure how
best to fix the problem...
Greg Von Kuster
On Feb 21, 2012, at 2:21
. For details about the various upload options to Galaxy data libraries,
see
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files.
For complete details about Galaxy data libraries, see
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries.
Greg
On Feb 10, 2012
and
needs no more description ! If not, please let me know the logs I should
look at and whatever else I should check.
Many thanks,
Greg E
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Port Jackson Bioinformatics
gedwar...@gmail.com
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Computer will be best for now.
Thanks (and also for being awake at 4am in Pennsylvania, if I have my time
zones right)
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 set far
it will be easier to do 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
Hi,
Still experimenting with Galaxy and Cloudman on AWS EC2.
The latest galaxy AMI is described
as 861460482541/galaxy-cloudman-2011-03-22.
How up to date is that Galaxy rev ?
Should I use hg to update it before running, or saving as a customised
Cloud AMI ?
Thanks.
--
Greg Edwards,
Port
as
the main run.
(Also, trivia dept, the doco in
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cversion_command.3E_tag_set
still references version_string instead of version_command. I
see
from a search of source code commits this name change was made in July
2011. )
Thanks !
Greg E
parent: 6160:70d41c4b591e
parent: 6159:eafac82b3767
user:John Chilton jmchil...@gmail.com
date:Mon Oct 24 15:36:24 2011 -0500
summary: Merging JJ fix with new branch
Let me know if other config info is important
--
Greg Edwards
gedwar...@gmail.com
Hello again,
In the picture below, it seems like the prompt for Autoscaling is obscuring
the colour legend for the server status icons.
Is there any way to show the legend ?
Thanks.
[image: load.png]
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gedwar...@gmail.com
your subscriptions to this and other Galaxy lists,please use the interface at:http://lists.bx.psu.edu/
Greg Von KusterGalaxy Development Teamg...@bx.psu.edu
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page ? I can't see a
Version/About type of item, either in menus or lurking in some rev stamp at
the bottom of pages etc.
Thanks.
--
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gedwar...@gmail.com
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Hello Greg,
Galaxy does not have versions as you'd find in commercial products. There is a
strict requirement that Galaxy provide reproducible behavior always, so any new
feature introduced into Galaxy (or any enhancement to an existing feature) must
not break any older feature that came
Greg,
Thanks. All clear.
It could be comforting for me to see a date stamp on that build number,
just to know I am using a recent build. But I'm sure you're following
normal practice.
When I fire up the Amazon Cloud service, using the recommended AMI
da58aab3 galaxy-cloudman-2011-03-22 (ami
Data libraries are accessible from the Shared Data pop-up menu in the top
Galaxy menu bar.
On Oct 28, 2011, at 1:12 PM, Oren Livne wrote:
Dear Greg,
Thanks so much, this helps a lot. I created a public data library, but it is
not listed in the list of libraries on the left pane
development plans for the
forsee-able future.
Thanks!
On Oct 25, 2011, at 4:30 AM, Anthony Underwood wrote:
HI Greg
Sorry for the confusion. The links are to screenshot uploads of Galaxy
showing the folder visibilities. If it’s still not clear please send a quick
mail.
Thanks Anthony
Hello Anthony,
On Oct 24, 2011, at 10:01 AM, Anthony Underwood wrote:
Hi Greg
Thanks for the reply. I can see now that as an admin user I can now add
private roles using the Admin View as opposed to the data libraries view.
It is still a bit unclear how a folder can be visible to one
I'm not following you here - please decipher your folder names, which I assume
are mapped to your encoded request strings.
On Oct 24, 2011, at 1:27 PM, Anthony Underwood wrote:
Thanks for the reply Greg
Still don’t think I’ve quite got it in my head though it’s becoming clearer.
I have 2
for some
time, but is not on our near-future plans for implementation.
Thank you,
Florent
Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
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Hello Florent,
Thanks for your comments and suggestions - see my inline comments.
On Oct 4, 2011, at 11:42 PM, Florent Angly wrote:
Hi Greg,
I have a few additional comments and questions though:
1/ In the universe_wsgi.ini file, maybe the tool_config_file parameter could
be renamed
Hello Louise-Amelie,
This behavior was corrected in change set 5612:3297ec86d657, which should be
available in the distribution within the next week or so. Sorry for the
inconvenience.
Greg Von Kuster
On Jun 20, 2011, at 11:06 AM, Louise-Amélie Schmitt wrote:
Hello everyone
, line 1867, in
_prepare_datasource_json_param_dict
rval[ key ] = self._prepare_datasource_json_list( val )
NameError: global name 'val' is not defined
Greg Von Kuster
On May 31, 2011, at 11:06 AM, Liisa Koski wrote:
I am also getting the same error with my local biomart and local galaxy
pull the fix from our development repo at
https://bitbucket.org/galaxy/galaxy-central.
Greg Von Kuster
On May 31, 2011, at 11:52 AM, Liisa Koski wrote:
Hi Greg,
I thought I was up to date. When I run the following command I get 'no
changes found'
hg incoming
real URL is https
in the script is 60. To remove
files from disk on the same day they were marked as deleted, override the
default by setting the -d flag to 0.
Greg Von Kuster
On Apr 30, 2011, at 4:59 PM, Simon Lank wrote:
Hi.
Our current galaxy database is ~ 600 gb, most of which are user deleted
datasets
to your tool_conf.xml file and start up
your Galaxy instance.
For details about adding a new tool, see
https://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial.
Greg Von Kuster
On Mar 26, 2011, at 10:19 AM, Andrea Edwards wrote:
Hello
I have looked at the biomart plugin for Galaxy
at:
http://lists.bx.psu.edu/
Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
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