Dear all,
I've uploaded to the test tool shed a pscan_chip_test repository and I'm
looking for help in testing it since it's my first time setting up a
Galaxy repository.
Pscan-ChIP is a motif enrichment analysis tool. The stand-alone web
interface is available here:
www.beaconlab.it/pscan
x.psu.edu List"
Sent: Thursday, October 16, 2014 3:17:39 PM
Subject: Re: [galaxy-dev] Help with Galaxy server migration
Hmm hopefully someone more knowledgeable about the tool shed than
me responds also but I had a couple quick thoughts.
The first is a warning - workflows may brea
Hmm hopefully someone more knowledgeable about the tool shed than
me responds also but I had a couple quick thoughts.
The first is a warning - workflows may break. At very least workflows
that depend on the previous instance having gone through tool
migrations instead of tool install. My under
Dear all,
I'm trying to migrate our local Galaxy server from a standalone server running
on CentOS 5 to a setup that runs Galaxy in a Docker container
(bgruening/galaxy-stable). Due to Docker and the setup of the container, almost
all data, tools, configs etc. have to move to a different place.
uration. They should also
only be used if you are attempting to set up "run jobs as the real user"
job running capabilities.
>>
>> > Further more when I want to kill my jobs by clicking
in galaxy web,the job keeps on running in my
background.I do not know how to fix thi
ng in my
> background.I do not know how to fix this.
> > Any help on this would be grateful.Thank you very much.
>
> Job deletion in the pbs runner was recently broken, but a fix for this bug
> will be part of the next stable release (on Monday).
>
> --nate
>
> >
Hi,
Thanks, great !, i'll try it.
Moussa.
Le Jeudi 24 avril 2014 17h47, Martin Čech a écrit :
Hi Moussa,
as Enis suggests please read the documentation and/or just call the API on your
local instance and see what it returns.
e.g. calling {{localhost}}/api/workflows?key={{API_key}} on my lo
Hi Moussa,
as Enis suggests please read the documentation and/or just call the API on
your local instance and see what it returns.
e.g. calling {{localhost}}/api/workflows?key={{API_key}} on my local
instance results in
https://gist.github.com/martenson/6b8e1d402fa193c914a5
Nice tool for callin
Hello,
Galaxy workflow and history structure is stored in Galaxy's database vs.
flat files so you can't just find the representation of those on the file
system.
I actually don't know if there is any documentation about the JSON
structure for those artifacts - I've CC'd the -dev mailing list so so
Hi,
will share mine in a few minutes off the list.
Cheers,
Bjoern
Am 28.03.2014 16:28, schrieb Luca Toldo:
Dear Galaxians,
I'd greatly appreciate if someone that has a running instance of galaxy
using local computing power and as well remote nodes (accessed with PBS
Pro) could share the files
Dear Galaxians,
I'd greatly appreciate if someone that has a running instance of galaxy
using local computing power and as well remote nodes (accessed with PBS
Pro) could share the files
universe_wsgi.ini
job_conf.xml
I've been trying very hard but failed to make noticeable progress.
I have a lo
I don't know of a way to accomplish what you are describing with the
tool framework - without prepopulating static files with all of the
data you will need - and even then I am not exactly sure what to do.
But it sounds like you would like to fetch this data from a database
or web service of some k
Hi,
I am doing a data transferring interface in galaxy. I want to accomplish
two things. First, when user enters a number, the interface will show some
related information or search results (eg, related files) by this unique
number. Then user can select the files they wanted to put into galaxy
his
Hi all,
we have installed a Galaxy istance on our server and we developed a new
workflow.
Also we have published this workflow and now is shared with every user.
How can we publish the workflow in only runnable mode and then make this
not editable for the other users?
Best regards
Pasquale
On Tue, Jan 14, 2014 at 2:17 PM, Pasquale Notarangelo
wrote:
> Hi all,
> we are two new galaxy users.
>
> We have developed 2 new tools and we would connect them into a new workflow.
>
> We are able to import both tools and to link them into a workflow but we
> aren't able to pass the output of th
Hi all,
we are two new galaxy users.
We have developed 2 new tools and we would connect them into a new
workflow.
We are able to import both tools and to link them into a workflow but we
aren't able to pass the output of the first tool as the input of the
second tool.
The first tool calls
Behalf Of Jennifer Jackson
Sent: Saturday, 4 January 2014 6:59 AM
To: Elsayed Hejazy
Cc: Galaxy Dev
Subject: Re: [galaxy-dev] Help Needed
Hello Elsayed,
Your protocol below seems to be a mix of a variant detection and an RNA-seq
workflow. To build a workflow for RNA-seq, you will want to compar
Hello Elsayed,
Your protocol below seems to be a mix of a variant detection and an
RNA-seq workflow. To build a workflow for RNA-seq, you will want to
compare your steps with the protocols in the link that I sent you.
If you want more examples, many more can be found here (for both RNA-seq
a
Hello Elsayed,
Protocol help for RNA-seq analysis can be found here:
https://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq
The QA/QC steps should be done before mapping, on individual datasets
(such as replicates) or on partial or merged datasets as needed (if that
is how th
i need to know more about the order of steps for RNA Seq data analysis
Is alignment and assembly should done first to combine all FASTQ reads into
one file and start analysis or i should do Quality Control ,filtering ,
trimming and manipulation first and do alignment and assembly at the end of
ana
hown_script">scripts/external_chown_script.py
> >
> >
> >
>
> The galaxy_external_* options are only supported with the drmaa plugin, and
> actually only belong in the univese_wsgi.ini for the moment, they have not
> been migrated to the new-style job
gt; > id="galaxy_external_chown_script">scripts/external_chown_script.py
>> >
>> >
>> >
>>
>> The galaxy_external_* options are only supported with the drmaa plugin,
>> and actually only belong in the univese_wsgi.ini for the
tyle job configuration. They should also
> only be used if you are attempting to set up "run jobs as the real user"
> job running capabilities.
>
> > Further more when I want to kill my jobs by clicking
> in galaxy web,the job keeps on running in my
> background.I do
Hi will see what the problem with sqlite is and give feedback later
On 8 August 2013 19:14, Nate Coraor wrote:
> On Aug 8, 2013, at 12:50 PM, Adam Brenner wrote:
>
> > The issue here is the last line:
> >
> > OperationalError: (OperationalError) disk I/O error u'PRAGMA
> > table_info("datas
On Aug 8, 2013, at 12:50 PM, Adam Brenner wrote:
> The issue here is the last line:
>
> OperationalError: (OperationalError) disk I/O error u'PRAGMA
> table_info("dataset")' ()
>
> Do you have any security rules setup on the server, quotes, disk
> issues, etc? You can always run a strace on run.
The issue here is the last line:
OperationalError: (OperationalError) disk I/O error u'PRAGMA
table_info("dataset")' ()
Do you have any security rules setup on the server, quotes, disk
issues, etc? You can always run a strace on run.sh for a better
understanding of whats going on.
--
Adam Brenne
To all,
I am getting the following error when I run sh run.sh :
galaxy.model.migrate.check DEBUG 2013-08-08 07:52:39,479 pysqlite>=2 egg
successfully loaded for sqlite dialect
Traceback (most recent call last):
File
"/scratch/sysusers/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py",
l
; in galaxy web,the job keeps on running in my
> background.I do not know how to fix this.
> Any help on this would be grateful.Thank you very much.
Job deletion in the pbs runner was recently broken, but a fix for this bug will
be part of the next stable release (on Monday).
--na
On Aug 7, 2013, at 7:55 AM, Jurgens de Bruin wrote:
> Hi,
>
> This is my first Galaxy installation setup so apologies for stupid questions.
> I am setting up Galaxy on a Cluster running Torque as the resource manager. I
> am working through the documentation but I am unclear on some things:
>
bject: [galaxy-dev] Help with cluster setup
Hi,
This is my first Galaxy installation setup so apologies for stupid questions. I
am setting up Galaxy on a Cluster running Torque as the resource manager. I am
working through the documentation but I am unclear on some things:
Firstly I am unable to
Hi,
This is my first Galaxy installation setup so apologies for stupid
questions. I am setting up Galaxy on a Cluster running Torque as the
resource manager. I am working through the documentation but I am unclear
on some things:
Firstly I am unable to find : *start_job_runners *within the
univer
Hi Huayan,
Your external website should accept a parameter "GALAXY_URL" and use this value
as e.g. the content of the attribute (use a sensible
default when not starting at Galaxy and this value is not provided). Your
webpage should post back to GALAXY_URL with a parameter named "URL" which
c
Hi,
I am trying to connect my local database/webpages to my local galaxy
server. But I have a hard to implement "send output to galaxy" function.
Right now I have a sending page to send a form to galaxy and it looks like
everything goes well. From the variable json_params(data_source.py), I can
se
Hello,
How can I change the "chromosome" name on a wig file to "chr"? FOr whatever
reason when I try feeding
this file with the program i am working with (CEAS package) it gives me an
error. But when I use a wig file
with chr it works fine
This is how my wiggle file looks like:
track type=wi
Hi Tilahun,
Are you using Ubuntu Precise 12.04? If so, I would highly recommend
taking a look at Debian Med's PPA[1]. I personally try to include and
keep updated as many tools used in Galaxy as possible in this PPA.
[1]https://launchpad.net/~debian-med/+archive/ppa
You can start using this PPA
Hi Tilahun,
What you can do is to download the tools and make symlinks to /usr/bin.
You can download bowtie (http://bowtie-bio.sourceforge.net/manual.shtml),
tophat (http://tophat.cbcb.umd.edu/) and cufflinks (
http://cufflinks.cbcb.umd.edu/). Then after decompressing it, enter your
terminal and
Yep, that's the primary issue with tophat not being found -- you'll need to
install binaries for some tools and potentially some reference genomes.
See the wiki page here for lots more information:
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
On Dec 18, 2012, at 11:48 AM, Tilahun Ab
Hi Dannon,
I tried to run Bowtie2 and Tophat using a reference from history and these
are the errors I got:
*An error occurred running this job: Error indexing reference sequence
/bin/sh: bowtie2-build: command not found.*
*
*
*
*
*An error occurred running this job: Could not determine Tophat ve
What specific errors are you seeing? Some tools have external dependencies
that need to be installed.
-Dannon
On Dec 18, 2012, at 11:29 AM, Tilahun Abebe wrote:
> Hi,
>
> We installed a local galaxy a couple of days ago following the basic
> installation instruction (http://wiki.galaxyproje
Hi,
We installed a local galaxy a couple of days ago following the basic
installation instruction (http://wiki.galaxyproject.org/Admin/Get%20Galaxy).
The installation went well, all the tools are listed on the left. I can
also upload data to Galaxy. However, an error occurs when I try to run
RNA-s
Hi Alfonso,
How did you launch your instance? Did you try using
http://usegalaxy.org/cloudlaunch
If not, give that a shot and see if you get up and going fine. If not,
please send another email and we'll figure it out there.
(I've CC-d galaxy-dev mailing list, which is the best place to get help o
Dear Galaxy help-centre
I want to use Tophat and Clifflinks to do an expression analysis. However, the
reference genome for Heterobasidion annosum (it is available at JGI) is not
listed. You have posted on your website that we can contact you if 'your
genome of interest' is not listed.
Is it
Quoting romain desprat (2012-07-26 13:49:02)
>galaxy ( on the linux partition). Unfortunately, galaxy doesn t have
>enough memory to work with this file.
Exactly what error is Galaxy reporting?
___
Please keep all replies on the lis
Quoting Rodrigo Faccioli (2012-07-26 00:08:23)
>I'd like to create a web-interface to run a C program. It is necessary a
>config file which is used as input to this program. Therefore, the values
You probably want to look at the element for the tool
configs:
http://wiki.g2.bx.psu.edu
Hi Tomithy,
Thank you so much your answer. I'll study this link.
Best regards,
--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structural Bioi
I am trying to work on 23 giga text file. My laptop being not powerful
enough I have split it in 10 files and made some modification on them. Now
I have made (linux and window) a double boot on my laptop and install
galaxy ( on the linux partition). Unfortunately, galaxy doesn t have enough
memory
Hi Rodrigo,
You can try this tutorial:
http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial
Although I dont do c/c++ development myself, you might want to want to make
sure that the c/c++ tools you create have been compiled for the platform
you are working on, especially when you switch fr
Hi,
I'm newbie in Galaxy. In fact, this is my first post.
I'd like to create a web-interface to run a C program. It is necessary a
config file which is used as input to this program. Therefore, the values
of parameters are informed by user through this web-interface. Its output
is some files.
I
Sir,
I would like to use PCA for a set of FASTA formatted 1400 sequences (in a
single file).I have stored all fasta formatted sequences in a text file. If
there is any problem for it, you can help me in doing the corresponding
analysis using R.
I am herewith giving a weblink for R, which uses
On 3/19/12 5:19 PM, Peter Cock wrote:
Why do you need to do anything special at all for Galaxy here? I'd
just write it as a single command line call which blocks. As far as
Galaxy will know it is just a slow tool.
I suppose the tool could just poll the server, and only produce results
when t
On 03/19/2012 10:19 PM, Peter Cock wrote:
On Mon, Mar 19, 2012 at 8:41 PM, Mark Johnson wrote:
I'm writing some tools to integrate NCBI data resources with Galaxy. I have
two questions.
The first is simple. I want to write a tool for a long-running process that
is handled by some other sched
On Mon, Mar 19, 2012 at 8:41 PM, Mark Johnson wrote:
> I'm writing some tools to integrate NCBI data resources with Galaxy. I have
> two questions.
>
> The first is simple. I want to write a tool for a long-running process that
> is handled by some other scheduler, and that produces its own job id
I'm writing some tools to integrate NCBI data
resources with Galaxy. I have two questions.
The first is simple. I want to write a tool for a long-running
process that is handled by some other scheduler, and that produces
its own job ids. Some web services,
Ok, I found the problem myself. I was totally searching in the wrong
place for the error. It was simply a syntax problem. The output
definition should be like follows:
I was closing the data tag too early.
On 10/06/2011 11:40 AM, Sarah Diehl wrote:
Hello,
I'm trying to write a wrapp
Hello,
I'm trying to write a wrapper for the intersectBed tool from the
BEDTools suite. The difficulty lies in the possible combinations of
input and output data formats. Input can be either bed or bam. When the
input is bed, the output is also bed. However, when the input is bam the
output c
On Jan 25, 2011, at 4:25 PM, Hans-Rudolf Hotz wrote:
> Have a look at the "galaxy_user" table to identify the 'broken' row, ie the
> wrong "e-mail".
>
>
> and then you can execute:
>
> update galaxy_user set email = "f...@fmi.ch" where email =
> "wrong_name@wrong_host.ch";
update galaxy_
On 01/25/2011 10:25 AM, Hans-Rudolf Hotz wrote:
On Jan 25, 2011, at 3:40 PM, Hans-Rudolf Hotz wrote:
[...]
Once again be careful with what you are doing, and don't blame me if you
create a mess ;)
-1-
PgAdmin ( http://www.pgadmin.org/ ) is a GUI application to manage Postgres
databases - it m
On 01/25/2011 03:44 PM, Davide Cittaro wrote:
On Jan 25, 2011, at 3:40 PM, Hans-Rudolf Hotz wrote:
Hi Davide
We were in a similar situation when we switched to external authentication.
Although, only one user was affected and we were using MySQL.
I could fix it by changing the contents of
On Jan 25, 2011, at 3:40 PM, Hans-Rudolf Hotz wrote:
> Hi Davide
>
> We were in a similar situation when we switched to external authentication.
> Although, only one user was affected and we were using MySQL.
>
> I could fix it by changing the contents of the "galaxy_user" with a few sql
> st
Hi Davide
We were in a similar situation when we switched to external
authentication. Although, only one user was affected and we were using
MySQL.
I could fix it by changing the contents of the "galaxy_user" with a few
sql statements. BUT, be careful! you can do a lot of damage to the datab
Dear all,
Our local galaxy instance uses apache authentication to log users. This said,
some users have no "User Name" and some other have a wrong "User name"
(probably because they have been added before the apache integration). I just
wonder if there's a way to modify the user names directly
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