Re: [galaxy-user] Teaching GALAXY

[Tilahun Abebe]

I also had a similar issue. I thought it has to do with the hurricane in
the east coat and never bothered to ask. Even small analyses (such as
running the RNA-seq analysis exercise by Jeremy Goecks) were stalled; in a
couple of instances for a day or more.

Thanks.

Tilahun
--

On Wed, Nov 7, 2012 at 2:57 PM, Larry Reiter  wrote:

>  Dannon,
>
> Thanks for getting back to me.  Both the local cloud install and the main
> server are frozen.  Well, not exactly frozen.  I can still rename or delete
> jobs, etc.  I can even switch histories and such, but I can't get it to run
> even simple jobs - like taking a demo file and running Fastq Groomer.  I
> realize the load is high today on the main server, but we were able to get
> jobs to run right up until we tried to MAP using Bowtie for Illumina.  At
> that point, all members of the class - and me - could not go any further
> (i.e. jobs are grey and never start to run).  Class ended almost three
> hours ago.
>
> Does this help?
>
> LTR
>
>
> On 11/7/12 2:52 PM, Dannon Baker wrote:
>
> Can you describe more about what is broken with your cloud install?
>
> Regarding main - the server has been under heavy load today and, while it 
> shouldn't remain frozen, might be slow to dispatch and, depending on the 
> type, execute) jobs.
>
> -Dannon
>
> On Nov 7, 2012, at 1:12 PM, Larry Reiter  
>  wrote:
>
>
>  Tried to teach a class today on ChipSeq analysis, but the local Cloud 
> install is broken and then the Penn server froze on us.  Is there something I 
> should know?
>
> LTR
>
> --
> Lawrence T. Reiter, Ph.D.
> Associate Professor, Department of Neurology
> 855 Monroe Ave., Link 415
> Memphis, TN 38163
> 901-448-2635 (Office)901-448-7440 (FAX)901-448-7443 (Lab)
> e-mail: lrei...@uthsc.edu
>
> Reiter Faculty Page
> Reiter Citation Index
> Tooth Study
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>
>
> --
> Lawrence T. Reiter, Ph.D.
> Associate Professor, Department of Neurology
> 855 Monroe Ave., Link 415
> Memphis, TN 38163
>
> 901-448-2635 (Office)
> 901-448-7440 (FAX)
> 901-448-7443 (Lab)
> e-mail: lrei...@uthsc.edu
>
> Reiter Faculty Page
> Reiter Citation 
> Index
> Tooth Study 
>
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[galaxy-user] Help on installing cutadapt

[Tilahun Abebe]

Hi Galaxy users,

I tried to install cutadapt for sequence trimming on a local Galaxy
instance. I successfully installed Galaxy as an administrator. However,
when Galaxy starts, I don't see the administrator option in the top menu
bar with the "Analyze Data, Workflow, Shared Data, Visualization, Help, and
User". It looks like the only way I can install cutadapt is with an
administrator option. Any suggestion how I can include the administrator
option in the menu?

Thanks for your help.

Tilahun
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Re: [galaxy-user] Loading files to local Galaxy

[Tilahun Abebe]

Thank you Paul and Nate. We will try the options you suggested.

One thing we found to work much faster (less than 5 minutes for most 
files) is to upload zipped data. Galaxy could upload and unzip the files 
without any problem. It doesn't seem any sequence data is lost. Has 
anyone tried this before?


Thanks.

Tilahun
---

Nate Coraor wrote:

Paul-Michael Agapow wrote:

From: Tilahun Abebe

We are trying to load Illumina data to our local Galaxy instance. The
files are between 700 MB and 2.2 GB. Files below 2 GB load in less

than

5 minutes. Files larger than 2 GB don't upload at all. We installed
Galaxy locally because we thought loading files will be faster than

the

server version. Any suggestions to solve this problem is highly

appreciated.

While  (from others experience) Galaxy _should_ be able to upload files
that large, we've had some problems with our local installation too.
Investigation didn't reveal any cause, so we put it down to the quality
of our network. You might what to look at the webserver or proxy that
you have in front of Galaxy - from memory, both Apache and nginx can be
configured to impose file size limits, so that _may_ be the problem. In
any event, you might want to configure your server to handle uploads and
downloads directly as per
<https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServe
r>. Finally you can pass an url to the upload dialog to get Galaxy to
pull the file from an ftp server - for example - and that may prove more
robust.

Hi Paul,

These failures may be due to the fact that many browsers will simply
fail to upload files>  2GB (although I know there are people out there
have successfully done it).

Tilahun, I'll echo Paul's suggestion to use the Production setup.  There
are also alternative options for getting data into Galaxy.  For users,
you can have an FTP server (or just a local directory on the server
where they can place files for upload):

   https://bitbucket.org/galaxy/galaxy-central/wiki/Config/UploadViaFTP

Or you can use data libraries and load directly off filesystems
accessible to the server:

   https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles

--nate



Paul Agapow (paul-michael.aga...@hpa.org.uk)
Bioinformatics, Centre for Infections, Health Protection Agency


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[galaxy-user] Loading files to local Galaxy

[Tilahun Abebe]

Hi guys,

We are trying to load Illumina data to our local Galaxy instance. The 
files are between 700 MB and 2.2 GB. Files below 2 GB load in less than 
5 minutes. Files larger than 2 GB don't upload at all. We installed 
Galaxy locally because we thought loading files will be faster than the 
server version. Any suggestions to solve this problem is highly appreciated.


Tilahun
---

John David Osborne wrote:
I noticed that for our new Ilumina data (which generate Sanger format) 
the FastQ groomer output is identical to the Ilumina FastQ input file.
I was hoping to go ahead and just use the raw FastQ files as input 
(saving disk space) for computing quality statistics to look at box 
plots, but it appears that the tool "Compute Quality Statistics" 
appears to require that the data have been run through FastQ Groomer 
first.
Is there a way to get around this and is this a bug? I assuming this 
is some sort of safety measure built into this tool?

-John


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