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:
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
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
@lists.bx.psu.edu List galaxy-dev@lists.bx.psu.edu
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
will be part of the next stable release (on Monday).
--nate
shenwiyn
From: Jurgens de Bruin
Date: 2013-08-07 19:55
To: galaxy-dev
Subject: [galaxy-dev] Help with cluster setup
Hi,
This is my first Galaxy installation setup so apologies for stupid
questions. I am setting up Galaxy
-dev
Subject: [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
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
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
Hi,
Thanks, great !, i'll try it.
Moussa.
Le Jeudi 24 avril 2014 17h47, Martin Čech mar...@bx.psu.edu 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
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
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
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
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
On Tue, Jan 14, 2014 at 2:17 PM, Pasquale Notarangelo
pasquale.notarang...@ba.infn.it 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
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
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 compare your
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
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
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
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
shenwiyn
From: Jurgens de Bruin
Date: 2013-08-07 19:55
To: galaxy-dev
Subject: [galaxy-dev] Help with cluster setup
Hi
, but a fix for this
bug will be part of the next stable release (on Monday).
--nate
shenwiyn
From: Jurgens de Bruin
Date: 2013-08-07 19:55
To: galaxy-dev
Subject: [galaxy-dev] Help with cluster setup
Hi,
This is my first Galaxy installation setup so apologies for stupid
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
shenwiyn
From: Jurgens de Bruin
Date: 2013-08-07 19:55
To: galaxy-dev
Subject: [galaxy-dev
Hi will see what the problem with sqlite is and give feedback later
On 8 August 2013 19:14, Nate Coraor n...@bx.psu.edu 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
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:
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
shenwiyn
From: Jurgens de Bruin
Date: 2013-08-07 19:55
To: galaxy-dev
Subject: [galaxy-dev] Help with cluster setup
Hi,
This is my first
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,
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 Brenner
To: galaxy-dev
Subject: [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
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
see
Hi Huayan,
Your external website should accept a parameter GALAXY_URL and use this value
as e.g. the content of the form action=xxx 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
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
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
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 tilahun.ab...@uni.edu wrote:
Hi,
We installed a local galaxy a couple of days ago following the basic
installation instruction
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
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
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 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
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 list
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
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
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 03/19/2012 10:19 PM, Peter Cock wrote:
On Mon, Mar 19, 2012 at 8:41 PM, Mark Johnsonmjohn...@ncbi.nlm.nih.gov 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
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
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,
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
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:
outputs
data name=output format=bed
change_format
when input=intype.bed value= format=bam/
/change_format
/data
/outputs
I
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
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