Dear Galaxy team,
I would like to upload a set of converter programs available for Generic
Feature Format (GFF).
When I tried to upload to Galaxy tool shed using my user name
vipin...@tuebingen.mpg.de, it gives me Server error message.
I am using a *.bz2 file for uploading. It will be great if
Hi Greg,
Regarding the tools contained in fml_gff_converter_programs.tar.bz2, the
following xml files are not well formed due to the malformed ! -- TODO
EDIT HERE tag:
fml_gff_converter_programs/galaxy/bed_to_gff3.xml
fml_gff_converter_programs/galaxy/gff3_to_bed.xml
Dear Galaxy Team,
As a part of in-house automated cleaning of data set from our production
galaxy service,
I am finding difficulty to get the galaxy assigned file name
(galaxy-root/database/001/dataset_001.dat)
for each data set from the corresponding database. We are using PostgreSQL
and
when I
Hi Branden,
I find a wiki documentation here,
https://bitbucket.org/galaxy/galaxy-central/wiki/DataTables
Hope this will help you to experiment a bit around.
regards, Vipin
Does anybody have any idea why I would be getting this error before the
tool runs?
--
Branden Timm
Great Lakes
. So, using that directory_hash_id function,
you should be able to reconstruct the full path to the file on disk with
just the unencoded dataset id and the root galaxy files directory prefix.
-Dannon
On Apr 25, 2011, at 4:16 PM, Vipin TS wrote:
Dear Galaxy Team,
As a part of in-house
Hi Branden,
Vipin, thanks for the tip. I was not aware of data tables at all.
I checked bwa_wrapper.xml and it is still using the from_file attribute for
the reference genome parameter, not from_data_table. It would appear then
that BWA is not using data tables? Additionally, I have now
Dear Galaxy Team,
I am switching our Galaxy production service to a new machine, We are using
Postgres as database server.
The existing database belongs to postgres version 8.3 and I took my
instance's dump using postgres version 8.4.
I am able to restore my database on postgres 8.4, Except few
Hello Nate,
When restoring, I generally use the --disable-triggers, which instructs
Postgres to ignore foreign key constraints.
--nate
Sorry for the relayed response from my side.
As you suggested I tried with --disable-triggers option for restoring the
database from the dump file,
Hello Nate,
Can you make sure that your dump was created with '-E UTF-8' flag?
I didn't use any customized encoding for my dump, took the default one, I
believe which is the database encoding.
Also, in your old database server, use psql's '\l' command to show the
encoding of your databases.
Hi Galaxy team,
I am experiencing a problem with visualizing my BAM files through Trackster
at my Galaxy instance. Please find the attached image along with this mail.
From the log file I am not seeing any clues about the error message which is
displayed on my browser page (A dependency (bai)
Hi Jeremy,
Are you able to visualize any BAM files in Trackster or do all files fail
with the same error? Were you able to visualize BAM files before you updated
your instance? Do you have SAMTools--which is required by
Trackster--installed and available via your path?
Yes, all BAM fails
Hi Kanwei,
Is this from a recent changeset that you pulled?
Yes I pulled on yesterday (6-7-2011)
--Vipin
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and other
Hi Jeremy,
Sorry for the delayed response from my side.
(1) click the pencil on a BAM dataset;
(2) try converting from BAM to BAI;
If the conversion failed, you should receive an informative error message
about why it's failing. Once you get this conversion to pass, you should be
able to
Server ErrorAn error occurred. See the error logs for more information.
(Turn debug on to display exception reports here)
My guess is that this will be a problem with your tool configuration file in
XML format.
-- Vipin
___
Please keep
Dear all,
I want to build a Galaxy tool to run R script.
Do you know if there is already such tool or similar function?
If you can share with me, I would very appreciate your help.
Hi Bo Liu,
In my Galaxy instance I added few tools running with R. Here I just wrote a
bash wrapper script to
Dear Kipper,
We are running most of our tools with the help of Shogun toolbox. Just
configure a recent version of Shogun toolbox to your local machine and add
the python path to your program. By doing this you will be able to call
shogun functionalities in your programs. (Depends on the
it as a dependency or 'egg'?
On Nov 28, 2011, at 2:28 PM, Vipin TS vipin...@gmail.com wrote:
Dear Kipper,
We are running most of our tools with the help of Shogun toolbox. Just
configure a recent version of Shogun toolbox to your local machine and add
the python path to your program. By doing
eager to see it in tool shed. I am
going to check tool shed frequently these days to get it asap.
Thanks
Lisa
On Wed, Feb 22, 2012 at 4:07 PM, Vipin TS vipin...@gmail.com wrote:
Hi,
We have the recent release version of DESeq at our Galaxy instance,
http
Hi Daniel,
On 22 March 2012 08:20, Daniel Sobral dsob...@igc.gulbenkian.pt wrote:
Hello,
At the moment I don't think there is a way to restrict usage of specific
tool(s) to specific user(s).
Is anyone thinking on developing this kind of functionality?
I guess it might be a bit complicated
On Thu, Feb 23, 2012 at 4:46 AM, Vipin TS vipin...@gmail.com wrote:
Hi Chris,
We are running DESEQ_VERSION 1.6.0 at our instance
http://galaxy.tuebingen.mpg.de/tool_runner?tool_id=deseq
thanks,
--Vipin T S
Which version of DESeq does this tool use?
Note
Hi Galaxy team,
I am trying to upload a tool wrapper to main tool shed
http://toolshed.g2.bx.psu.edu and ending up with a 'server error' message.
Could you please let me know what is going wrong here.
thanks,
--Vipin
___
Please keep all
on your local instance, please read the following:
http://wiki.g2.bx.psu.edu/Admin/Interface
--Vipin
On 24 August 2012 13:09, kauerb...@comcast.net wrote:
Hello,
Can you tell me how to become an 'admin' user on Galaxy, or else change
the current admin?
Thank you.
-Ken.
Hi Galaxy team,
Can I use a single database connection to serve multiple Galaxy instance ?
thanks,
--Vipin
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and other
Hello members,
I believe currently there is no process to validate email address provided
during user account creation. We are experiencing a huge fake account
creation attack on our public facing galaxy
instancehttp://galaxy.raetschlab.org
.
Does anybody who has been managing a public instance,
Hello members,
On my new server machine I have configured apache server along with
mod_security. Now I would like to place my Galaxy installation behind
apache and is there any detailed explanation to describes the steps.
I am following the galaxy wiki
Hello dev-members,
We are trying to place our public Galaxy
instancehttp://galaxy.raetschlab.orgin a more secured manner,
Currently I am playing with few test cases about
the redirection vulnerabilities.
The following link uses a URL variable called “redirect_url” to redirect a
user to a given
/
Thanks,
--/Vipin
Rätschlab, Computational biology dept.
Memorial Sloan-Kettering Cancer Center
On Tue, Mar 12, 2013 at 8:15 AM, Paul Boddie paul.bod...@biotek.uio.nowrote:
On 11/03/13 23:20, Vipin TS wrote:
On my new server machine I have configured apache server along with
mod_security
12, 2013, at 12:08 PM, Vipin TS wrote:
Hello dev-members,
We are trying to place our public Galaxy
instancehttp://galaxy.raetschlab.org/in a more secured manner, Currently I
am playing with few test cases about
the redirection vulnerabilities.
The following link uses a URL variable called
Dear dev-team,
I am interested to implement the secure hashed password specifically
SHA-256 or greater to the galaxy users using publicly available python
module PBKDF2.
I have a piece of python code which will do the job but not quite sure how
I can integrate this to my local galaxy code
Hello dev-team,
I would like to add the different type of password encryption to the users
in my galaxy instance. I started working with the current password encoding
script:
/home/apps/galaxy-dist/lib/galaxy/util/hash_util.py
I will keep the current sha1 and add another layer of encryption to
changes.
I'd be happy to see this go into main with sha256 or something
similar. Also, we could consider adding a random per-user salt field
if you are really concerned about this.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, May 2, 2013 at 10:21 AM, Vipin TS vipin
Hi dev-team,
We have placed our galaxy instance ssl and I need to make sure that the
secure flag is set
on the cookie (commonly represented by the word “secure” under the Security
column) but
I am not able to do the same. something like below:
[image: Inline image 2]
when I checked on my
with sha256 or something
similar. Also, we could consider adding a random per-user salt field
if you are really concerned about this.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, May 2, 2013 at 10:21 AM, Vipin TS vipin...@gmail.com wrote:
Hello dev-team,
I would like
:21 AM, Vipin TS vipin...@gmail.com wrote:
Hello dev-team,
I would like to add the different type of password encryption to the
users
in my galaxy instance. I started working with the current password
encoding
script:
/home/apps/galaxy-dist/lib/galaxy/util/hash_util.py
I will keep
Hello,
I figured out the place where the cookie gets set in Galaxy and then add
secure to that. Apache configuration didn't work well.
added the following code into function set_cookie in:
lib/galaxy/web/framework/__init__.py
*def set_cookie( self, value, name='galaxysession', path='/',
compatible way, and I think it is a
good idea so I will be committing it to central shortly.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, May 2, 2013 at 2:34 PM, Vipin TS vipin...@gmail.com wrote:
Thanks James, I have updated the password of one user
Hello dev-team,
Usually when I want to move a Galaxy Published Page between instances I
follows these steps:
(a) moving workflows and dataset from instance_1 to instance_2
(b) run the workflow at instance_2
(c) create the page at instance_2
So my question is - Can I move/share published pages
Hello dev-team,
I am trying to upgrade our production instance to the latest release
(to galaxy-dist) , somehow I am not able to restart the instance. Here
is the log message I found:
File ./scripts/paster.py, line 35, in module
serve.run()
File
Hello dev-team,
I have updated
code repository
of our production instance https://galaxy.cbio.mskcc.org to the recent
galaxy-dist (10216:ebe87051fadf), now the instance page it is not rendering
in a proper way.
The error message I can see from the log file as follows:
Hello dev-team,
I am experiencing a strange problem with my production instance, after I
carefully merged remote changes from galaxy-dist release to my code
repository. While restarting, It fails to load the the page properly, the
message from log file stating that serving on 0.0.0.0:8080
Here
:
Hi Vipin,
This has been fixed in the stable branch of galaxy-central
https://bitbucket.org/galaxy/galaxy-central/commits/cd6fec2f5cba but has
not made it on to galaxy-dist yet.
Thanks for using Galaxy,
Dan
On Aug 9, 2013, at 2:33 PM, Vipin TS wrote:
Hello dev-team,
I am
directory
(i.e.
/codebase/database/compiled_templates/*)?
Thanks for using Galaxy,
Dan
On Aug 9, 2013, at 3:22 PM, Vipin TS wrote:
Hi Dan,
Thanks for the information, I have updated this to my repository manually.
Now I can invoke the page but the frames were not loaded correctly.
The log
--/Vipin
-- Forwarded message --
From: Vipin TS vipin...@gmail.com
Date: Fri, Aug 9, 2013 at 5:04 PM
Subject: Re: [galaxy-dev] Public production instance page is not rendering
properly
To: Daniel Blankenberg d...@bx.psu.edu
Hi Dan,
Thanks for your support, Hmm, I can see
to the file in the repository? What is the output
of:
hg diff templates/webapps/galaxy/root/history.mako
and
hg summary
and
hg config
Thanks for using Galaxy,
Dan
On Aug 9, 2013, at 3:56 PM, Vipin TS wrote:
Hi Dan,
I deleted the
contents from
/codebase/database/complied_templates
Please follow the session Keep your code up to date at
http://wiki.galaxyproject.org/Admin/Get%20Galaxy
--/Vipin
On Tue, Aug 27, 2013 at 10:58 AM, Richard Kuo izen...@gmail.com wrote:
I can't seem to find any information on the Galaxy wiki website about the
procedure for updating a local
Hello,
I am slightly confused with adding a new genome to my local Galaxy
instance, I am using the recent default branch 10411:c42567f43aa7
(following the documentation at
http://wiki.galaxyproject.org/Admin/Data%20Integration)
I have edited the ~/galaxy-dist/tool-data/all_fasta.loc to add new
H
i Jen Ricardo,
Thanks for the suggestions. It is resolved now. The problem was due to the
tab delimiter.
In my local workstation the tab was preset to four spaces.
regards, Vipin
Is it not showing up under the list of databases/genomes when you at
these locations:
1 - Get Data -
Hello Rui,
We have DESeq2 wrapper in our oqtans package and you will find this at
https://github.com/ratschlab/oqtans_tools/tree/master/DESeq2
I am currently creating the associated tool_dependency.xml file for dumping
the package in galaxy toolshed. otherwise it requires some manual effort to
Yes I am agreeing on all statements.
Let me finish my package and will add in one of the toolshed by today
evening. I also willing to test other wrappers to improve the additional
parameter settings.
Tool wrappers Work In Progress from my side:
DEXSeq
edgeR
Scripture
STAR aligner
SAFT multi
Hi
Stanislas,
Please check the PATH variable and make sure that you can access bowtie2
from command line and then restart the Galaxy service through cloudman
interface. I think that should work.
Vipin
I'm trying to run Galaxy on an Amazon AWS cloud using the normal Cloudman
distribution
with the
EBI server or within galaxy?
I am not sure, can you please paste the url which points to the file.
Thanks for any help.
On Oct 14, 2013, at 5:50 PM, Vipin TS wrote:
Hi
Stanislas,
Please check the PATH variable and make sure that you can access bowtie2
from command line
/
Cheers,
Enis
On Mon, Oct 14, 2013 at 10:06 PM, Vipin TS vipin...@gmail.com wrote:
Hi dev-team,
I am trying to launch cloudman on AWS us-east-1a and I am getting the
message
*All cluster services started; the cluster is ready for use.
(2013-10-14 19:45:52)*
I am seeing some error
Hi,
I am the author for fml_gff3togtf tool package, currently merged into our
instance at
http://galaxy.cbio.mskcc.org, The tool can be accessed with following link:
https://galaxy.cbio.mskcc.org/tool_runner?tool_id=fml_gff2bed
--/Vipin
Sloan-Kettering Institute
http://galaxy.cbio.mskcc.org
On
filter type=param_value ref=inputmodel column=2/
filter type=param_value ref=inputSize column=3/
If you closely look at the above line the double quotes are different for
column field.
filter type=param_value ref=inputRealization column=4
/
On Thu, Mar 13, 2014 at 5:32 PM, Wang, Xiaofei xfw...@ku.edu wrote:
Hi Folks,
I figured out the problem of tool dependencies successfully. The
installation status is installed for all tool sheds. The tools are also
shown on left tool panel. But, I got problems when I used the tool sheds to
Hello dev-team,
With the current state, is it possible to write an interactive page for a
tool in Galaxy?
In my case, I m considering to build a tool page with JavaScript embed in
XML file, my expectation is to behave the Galaxy tool page as google
translate page with option instant translation
cards:
https://trello.com/c/VizlCET9
https://trello.com/c/phMelslw
Ciao,
Bjoern
Am 04.06.2014 18:33, schrieb Vipin TS:
Sorry for re-posting! any suggestions to make an interactive tool page.
Thanks you, Vipin
On Tue, May 20, 2014 at 5:25 PM, Vipin TS vipin...@gmail.com wrote:
Hello
Hi Greg,
When I trying to upload a next release version o my
https://toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf converter
program to Community Toolshed, I am getting an internal error message.
I am uploading a tar.gz file to the page https://toolshed.g2.bx.psu.edu/
but this fails.
Could
Hey Greet and Bjoern,
Sorry for the troubles with dependencies during the automated installation
procedure!
I will add tool dependency file, when I get some time during this weekend
:)
Vipin | Rätsch Lab
On Tue, Jul 29, 2014 at 10:06 AM, Björn Grüning bjoern.gruen...@gmail.com
wrote:
Hi
Hi all,
I do have a version 0.1 wrapper for STAR under our oqtans package, however
it is not yet in toolshed.
https://github.com/ratschlab/oqtans_tools/tree/master/STAR/2.3/
Feel free to comment,
Vipin | Rätsch Lab
On Wed, Sep 24, 2014 at 4:55 PM, Curtis Hendrickson (Campus)
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