from:"Todd Oakley"

[galaxy-dev] Problem with Tools in Workflow Editor

2014-04-04 Thread Todd Oakley


Hi All,
I posted this earlier in the week, but haven't heard anything. I 
changed the title of the email to hopefully attract more attention.


We are getting errors when creating a workflow. Some of the tools, 
when selected, say only error loading field data. As such, we cannot 
use them in workflows, even though the tools work fine in Analyze Data.


This seems like it is correlated with the fact that we developed 
these tools, and changed their names along the way. If this is the 
cause, one solution could be for us to clear Tool Versions/Version 
lineage in our galaxy instance. Is there a way to clear our cluttered 
tool lineages?



Thanks for any insights,

Todd Oakley, UCSB
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[galaxy-dev] Error Loading Field Data

2014-03-31 Thread Todd Oakley


Hi All,
We are getting errors when creating a workflow. Some of the tools, 
when selected, say only error loading field data. As such, we cannot 
use them in workflows, even though the tools work fine in Analyze Data.


This seems like it is correlated with the fact that we developed 
these tools, and changed their names along the way. If this is the 
cause, one solution could be for us to clear Tool Versions/Version 
lineage in our galaxy instance. Is there a way to clear our cluttered 
tool lineages?



Thanks for any insights,

Todd Oakley, UCSB
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[galaxy-dev] SRA datatype

2014-02-07 Thread Todd Oakley

Hello,
I am seeking advice on how to add the SRA datatype to Galaxy. We want 
to download data from NCBI that is in SRA format, and can no longer have the 
NCBI site convert it to fastq. I am not experienced with adding file types, to 
rudimentary advice would be most appreciated.

Thanks,
Todd Oakley, UCSB
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Re: [galaxy-dev] Opinions on organizing tools into repos

2012-10-30 Thread Todd Oakley


James,
Yes, I think discovery is the main problem, and your suggestion 
would help.  I suppose having conventions would also help discovery and 
understanding in general, but that is difficult to achieve in a 
community-based project.

Todd


On 10/30/2012 8:00 AM, James Taylor wrote:

On Mon, Oct 29, 2012 at 9:23 PM, Todd Oakley
todd.oak...@lifesci.ucsb.edu wrote:

We've developed a large number of tools to allow my lab to conduct
phylogenetic analyses in Galaxy. Inspired by the mothur package in Galaxy,
which is all in one repo, I made the decision to add all our related tools
to 1 repo on the tool shed. However, it seems that makes individual tools
like raxml difficult to find for other users.

Todd, I prefer bundling related tools (and other assets) in repositories.

If the problem is discovery perhaps we can fix this in the toolshed UI
by adding the ability to browse for tools directly in addition to
browsing for repositories?
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--

***
Todd Oakley, Professor
Ecology Evolution and Marine Biology
University of California, Santa Barbara
Santa Barbara, CA 93106 USA
***

Lab Website http://labs.eemb.ucsb.edu/oakley/todd/
Twitter: @UCSB_OakleyLab

*Recent Papers: *

 * Pancrustacean Phylotranscriptomics
   MBE Paper
   
http://mbe.oxfordjournals.org/content/early/2012/09/12/molbev.mss216.abstract

 * Convergent Evolution in Cephalopoda
   BMC Ev Biol http://www.biomedcentral.com/1471-2148/12/129/abstract
 * Cnidocyte discharge regulated by opsin and light
   BMC Biology Paper http://tinyurl.com/7dajl2q Scientific American
   Write-up
   
http://blogs.scientificamerican.com/science-sushi/2012/03/05/hydra-watch-what-they-eat/

 * Sponge Larvae Could be Guided by Cryptochrome
   J Exp Biol. Paper http://jeb.biologists.org/content/215/8/ii |
   Nature News
   http://www.nature.com/nature/journal/v484/n7393/full/484145d.html

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Re: [galaxy-dev] MrBayes wrapper - set parameters through Galaxy?

2012-10-29 Thread Todd Oakley


Ann,
Also to your request I'd appreciate any input about MrBayes or a 
similar kind of tool.


We are developing a suite of tools for phylogenetics in Galaxy. We are 
calling the tool suite Osiris.


We are currently adding the full tool suite to Bit Bucket:
https://bitbucket.org/repo/all?name=osiris_phylogenetics

and many tools are on the tool shed under a repository called 
ucsb_phylogenetics.


We are describing some of the tools here:

http://osiris-phylogenetics.blogspot.com/



We are in rather active development right now, but the RAxML tools have been 
used rather extensively, and allow some interactive choices (model choice, 
bootstrap reps, DNA v Protein, etc).  We also have a tool for BEAST (very 
simple, just passes the formatted xml file to run the program through Galaxy).  
Another phylogenetic tree estimation tool on the tool shed (not ours) exists 
for GARLI.

We plan to develop a tool for MrBayes, as well, but perhaps we will not have to 
anymore!


Best wishes,

Todd Oakley


On 10/29/2012 11:43 AM, Gomez, Ann wrote:

Brilliant, thanks! I had seen the FAQ, but didn't know about configfiles. Much 
appreciated!

Ann


-Original Message-
From: ja...@taylorlab.org [mailto:ja...@taylorlab.org] On Behalf Of James Taylor
Sent: Monday, October 29, 2012 2:03 PM
To: Gomez, Ann
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] MrBayes wrapper - set parameters through Galaxy?

Ann,

I think you may be able to do this by generating another nexus file using 
configfiles in the Galaxy tool config which just contains a command block, 
similar to the example here:

   
http://mrbayes.sourceforge.net/wiki/index.php/FAQ#How_do_I_run_MrBayes_in_batch_mode.3F

-- jt


On Mon, Oct 29, 2012 at 1:24 PM, Gomez, Ann ann.go...@agr.gc.ca wrote:

Hello all,



I've written a MrBayes wrapper that accepts a Nexus file (presumably
containing a data block and a command block). In order to make it a
bit easier for new users, I was hoping to be able to  let users
specify some parameters, such as their model, in Galaxy, as opposed to
including it in the command block of the Nexus file. Am I correct in
thinking this is not possible since MrBayes does not have a way to invoke 
commands in-line?



To clarify for non-MrBayes people, my limited understanding is that
you either invoke  the interpreter with $ mb and then enter your
commands, or directly execute a Nexus file (containing the data and
commands) with  $ mb nexusfilename.



Please correct me if I'm missing something or thinking about this
completely wrong. I'd appreciate any input about MrBayes or a similar kind of 
tool.



Cheers,

Ann



Ann Gomez

Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire
Canada

KW Neatby Bldg | éd. KW Neatby
960 Carling Ave| 960, avenue Carling
Ottawa, ON | Ottawa (ON) K1A 0C6
E-mail Address / Adresse courriel: ann.go...@agr.gc.ca Telephone |
Téléphone 613-759-6805 Facsimile | Télécopieur 613-759-1701 Government
of Canada | Gouvernement du Canada




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--

***
Todd Oakley, Professor
Ecology Evolution and Marine Biology
University of California, Santa Barbara
Santa Barbara, CA 93106 USA
***

Lab Website http://labs.eemb.ucsb.edu/oakley/todd/
Twitter: @UCSB_OakleyLab

*Recent Papers: *

 * Pancrustacean Phylotranscriptomics
   MBE Paper
   
http://mbe.oxfordjournals.org/content/early/2012/09/12/molbev.mss216.abstract

 * Convergent Evolution in Cephalopoda
   BMC Ev Biol http://www.biomedcentral.com/1471-2148/12/129/abstract
 * Cnidocyte discharge regulated by opsin and light
   BMC Biology Paper http://tinyurl.com/7dajl2q Scientific American
   Write-up
   
http://blogs.scientificamerican.com/science-sushi/2012/03/05/hydra-watch-what-they-eat/

 * Sponge Larvae Could be Guided by Cryptochrome
   J Exp Biol. Paper http://jeb.biologists.org/content/215/8/ii |
   Nature News
   http://www.nature.com/nature/journal/v484/n7393/full/484145d.html

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[galaxy-dev] Opinions on organizing tools into repos

2012-10-29 Thread Todd Oakley


Thanks Dannon for adding the Phylogenetics category,
I changed the name of this thread, to go in a related by new direction:

I wonder if the Galaxy developers and community have any opinions on 
what is the best way to organize tools into repositories. We've 
developed a large number of tools to allow my lab to conduct 
phylogenetic analyses in Galaxy. Inspired by the mothur package in 
Galaxy, which is all in one repo, I made the decision to add all our 
related tools to 1 repo on the tool shed. However, it seems that makes 
individual tools like raxml difficult to find for other users.  
Recently, we started putting these tools on to bitbucket, and organizing 
them in different categories (alignment, phylogenetics, orthologies, 
etc), which is a compromise between all-in-one-repo and each-its-own-repo.


The thing is that many of the tools do not stand alone, and really are 
designed to function with other tools in the package. Any philosophies 
or opinions are welcome, as I feel like I have not come to a good 
solution on this...


Todd




On 10/29/2012 1:50 PM, Dannon Baker wrote:

On Oct 29, 2012, at 4:40 PM, Oleksandr Moskalenko o...@hpc.ufl.edu wrote:


This is an interesting project. I'm glad to see more people working on phylogenetics 
related wrappers and workflows. I wonder if we could get a Phylogenetics 
category added to the main Galaxy Toolshed, so we could put all the relevant wrappers in 
there to make them easier to find considering the apparent duplication of efforts.

Good idea, the main toolshed now has a Phylogenetics category.

-Dannon
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--

***
Todd Oakley, Professor
Ecology Evolution and Marine Biology
University of California, Santa Barbara
Santa Barbara, CA 93106 USA
***

Lab Website http://labs.eemb.ucsb.edu/oakley/todd/
Twitter: @UCSB_OakleyLab

*Recent Papers: *

 * Pancrustacean Phylotranscriptomics
   MBE Paper
   
http://mbe.oxfordjournals.org/content/early/2012/09/12/molbev.mss216.abstract

 * Convergent Evolution in Cephalopoda
   BMC Ev Biol http://www.biomedcentral.com/1471-2148/12/129/abstract
 * Cnidocyte discharge regulated by opsin and light
   BMC Biology Paper http://tinyurl.com/7dajl2q Scientific American
   Write-up
   
http://blogs.scientificamerican.com/science-sushi/2012/03/05/hydra-watch-what-they-eat/

 * Sponge Larvae Could be Guided by Cryptochrome
   J Exp Biol. Paper http://jeb.biologists.org/content/215/8/ii |
   Nature News
   http://www.nature.com/nature/journal/v484/n7393/full/484145d.html

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[galaxy-dev] Jobs crash only in workflow context

2012-10-16 Thread Todd Oakley


Hello,
We just did a few tweaks to improve Galaxy performance, and a new 
issue popped up that I would like advice on troubleshooting.


When we run workflows, we see that tools later in the workflow run 
and crash before the results they depend on have completed running.


We can re-run the crashed jobs later and they work fine, suggesting 
that they are only failing in the context of running workflows.


I'd appreciate any advice on how to start troubleshooting this problem.

Thanks much!
Todd


--

***
Todd Oakley, Professor
Ecology Evolution and Marine Biology
University of California, Santa Barbara
Santa Barbara, CA 93106 USA
***

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[galaxy-dev] ERROR on History export

2012-04-25 Thread Todd Oakley


Hello,
I'd am trying to export histories to upload to another galaxy instance.

For some histories, it works fine.  However, for others, I get an 
error.  When I turn on debug, I get the error pasted below.  Any 
thoughts on what is the cause of object has no attribute 'hid'?


Thanks!
Todd



 Server Error

Module paste.exceptions.errormiddleware:*143* in |__call__|
| http://knot.cnsi.ucsb.edu:8080/history/export_archive#app_iter *=* 
self*.*application*(*environ*,* start_response*)*|

Module paste.debug.prints:*98* in |__call__|
| http://knot.cnsi.ucsb.edu:8080/history/export_archive#environ*,* 
self*.*app*)*|

Module paste.wsgilib:*539* in |intercept_output|
| http://knot.cnsi.ucsb.edu:8080/history/export_archive#app_iter *=* 
application*(*environ*,* replacement_start_response*)*|

Module paste.recursive:*80* in |__call__|
| http://knot.cnsi.ucsb.edu:8080/history/export_archive#*return* 
self*.*application*(*environ*,* start_response*)*|

Module paste.httpexceptions:*632* in |__call__|
| http://knot.cnsi.ucsb.edu:8080/history/export_archive#*return* 
self*.*application*(*environ*,* start_response*)*|

Module galaxy.web.framework.base:*145* in |__call__|
| http://knot.cnsi.ucsb.edu:8080/history/export_archive#body *=* 
method*(* trans*,* kwargs *)*|

Module galaxy.web.controllers.history:*591* in |export_archive|
| 
http://knot.cnsi.ucsb.edu:8080/history/export_archive#history_exp_tool*.*execute*(* 
trans*,* incoming *=* params*,* set_output_hid *=* True *)*|

Module galaxy.tools:*1276* in |execute|
| http://knot.cnsi.ucsb.edu:8080/history/export_archive#*return* 
self*.*tool_action*.*execute*(* self*,* trans*,* incoming*=*incoming*,* 
set_output_hid*=*set_output_hid*,* history*=*history*,* kwargs *)*|

Module galaxy.tools.actions.history_imp_exp:*103* in |execute|
| 
http://knot.cnsi.ucsb.edu:8080/history/export_archive#include_deleted*=*incoming*[* 
'include_deleted' *]* *)*|

Module galaxy.tools.imp_exp:*419* in |setup_job|
| 
http://knot.cnsi.ucsb.edu:8080/history/export_archive#input_datasets 
*=* *[* assoc*.*dataset*.*hid *for* assoc *in* job*.*input_datasets *]*|

*AttributeError: 'NoneType' object has no attribute 'hid'*
--

***
Todd Oakley, Professor
Ecology Evolution and Marine Biology
University of California, Santa Barbara
Santa Barbara, CA 93106 USA
***

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[galaxy-dev] Create and Transfer Galaxy Page

2012-04-17 Thread Todd Oakley


Hi all,
[Not sure if this is better suited to galaxy-dev or -user, so I'm 
sending to both].


I want to document some Galaxy analyses and results for a paper I'm 
submitting - something like the 'Windshield Splatter' supplement: 
https://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter.



My question is - can I create a Galaxy 'Published Page' from my local 
Galaxy instance/histories, and then transfer that page to the main 
Galaxy instance? The reason is that I cannot make my local Galaxy 
instance public, as I am using a campus resource to host our galaxy.  If 
this is possible, how can I do that?  If not, any other ideas? Also, are 
there any tutorials/pages on how to create Published Pages in Galaxy in 
the first place?


Thanks for reading and best wishes,

Todd

--

***
Todd Oakley, Professor
Ecology Evolution and Marine Biology
University of California, Santa Barbara
Santa Barbara, CA 93106 USA
***

Lab Website http://labs.eemb.ucsb.edu/oakley/todd/
Twitter: @UCSB_OakleyLab

*Recent Papers: *

 * Cnidocyte discharge regulated by opsin and light
   BMC Biology Paper http://tinyurl.com/7dajl2q | Scientific American
   Write-up
   
http://blogs.scientificamerican.com/science-sushi/2012/03/05/hydra-watch-what-they-eat/

 * Sponge Larvae Could be Guided by Cryptochrome
   J Exp Biol. Paper http://jeb.biologists.org/content/215/8/ii |
   Nature News
   http://www.nature.com/nature/journal/v484/n7393/full/484145d.html

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[galaxy-dev] Fwd: Create and Transfer Galaxy Page

2012-04-17 Thread Todd Oakley




Hi all,
[Not sure if this is better suited to galaxy-dev or -user, so I'm 
sending to both].


I want to document some Galaxy analyses and results for a paper I'm 
submitting - something like the 'Windshield Splatter' supplement: 
https://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter.



My question is - can I create a Galaxy 'Published Page' from my local 
Galaxy instance/histories, and then transfer that page to the main 
Galaxy instance? The reason is that I cannot make my local Galaxy 
instance public, as I am using a campus resource to host our galaxy.  If 
this is possible, how can I do that?  If not, any other ideas? Also, are 
there any tutorials/pages on how to create Published Pages in Galaxy in 
the first place?


Thanks for reading and best wishes,

Todd

--

***
Todd Oakley, Professor
Ecology Evolution and Marine Biology
University of California, Santa Barbara
Santa Barbara, CA 93106 USA
***

Lab Website http://labs.eemb.ucsb.edu/oakley/todd/
Twitter: @UCSB_OakleyLab

*Recent Papers: *

 * Cnidocyte discharge regulated by opsin and light
   BMC Biology Paper http://tinyurl.com/7dajl2q | Scientific American
   Write-up
   
http://blogs.scientificamerican.com/science-sushi/2012/03/05/hydra-watch-what-they-eat/

 * Sponge Larvae Could be Guided by Cryptochrome
   J Exp Biol. Paper http://jeb.biologists.org/content/215/8/ii |
   Nature News
   http://www.nature.com/nature/journal/v484/n7393/full/484145d.html

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Re: [galaxy-dev] Possible Galaxy memory leak?

2012-03-06 Thread Todd Oakley

We've experience memory-leak symptoms and we also use the PBS job runner 
here.  We did not try to locate the leak, but instead installed monit as 
a work-around


http://mmonit.com/monit/
Todd Oakley

On 3/6/2012 11:10 AM, Nate Coraor wrote:

There is also a memory leak that occurs when using the pbs job runner.  I 
believe the leak is somewhere in libtorque or pbs_python but I have not yet 
tracked it down.

--nate

On Feb 29, 2012, at 3:28 PM, John Chilton wrote:


We had intermittent issues like this for an embarrassingly long time
at MSI, but since we applied this patch
https://bitbucket.org/galaxy/galaxy-central/pull-request/36/fix-for-dynamic_optionspy
Galaxy has been running smoothly for weeks. Seems unlikely this is the
problem in your case (unless you have pulled in tools with make use of
dynamic options), but it something to consider.

-John

On Wed, Feb 29, 2012 at 2:08 PM, Joshua Grossgros...@students.wwu.edu  wrote:

Hi all--

Our group is running a local instance of Galaxy on a Linux box.  We have
been noticing a memory issue, where if we leave the server running for a few
days, soon all available memory (~8gb) will be used up to the point where
the tools fail because they are unable to allocate new memory.

While we haven't done any rigorous testing, this issue seems to be
independent of the specific tools we run, and actually seems to still appear
if we do not run any tools at all.  The process python is what is taking
up all the memory, and the issue is not instantaneous but happens over
time.  Restarting the server frees the memory immediately.

Is this a known issue?  If so, is there a known fix for it?  Any insight on
this would be much appreciated, as it is complicating our efforts to
automate long work-flows.

Thank you so much for your time

Josh Gross, Western Washington University.

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--
*
Todd Oakley, Professor
Ecology Evolution and Marine Biology
University of California, Santa Barbara
Santa Barbara, CA 93106 USA

NEWLY UPDATED LAB WEBSITE: http://labs.eemb.ucsb.edu/oakley/todd/
**

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[galaxy-dev] fastq_pe_even.pl

2011-10-22 Thread Todd Oakley

I'm trying to install preppereadsforveletfasta

to prepare velvet-style fastq files.  However, it seems to need a perl script 
that I cannot find

fastq_pe_even.pl


Does anyone know where I can get this?

Thanks,
Todd Oakley
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[galaxy-dev] fastqc in local galaxy - problem

2011-10-19 Thread Todd Oakley

Hi all,
I am setting up our own galaxy instance here (or trying to). We'd
like to use fastqc, but I have run into a problem implementing it. Any
suggestions would be most welcome, as to what might be wrong.

1. fastqc runs fine outside of galaxy. But when I try the same file
inside galaxy, I get errors.

2. I can look to the shell script generated by galaxy inside
~/galaxy-dist/database/pbs/ . When I run that python command inside the
sh script, generated by galaxy, to execute fastqc -- it works fine,
without errors.

Therefore, it seems as if there is some sort of permission or path
problem when galaxy runs fastqc. I have fastqc in the main path, and
also installed it in the jars directory where the fastqc tool looks
for it. However, I still can't understand this, since when outside of
galaxy, I can run the python command generated by galaxy successfully.

The output/error inside galaxy is here:

Exception in thread main java.lang.NoClassDefFoundError:
uk.ac.bbsrc.babraham.FastQC.Sequence.FastQFile
at java.lang.Class.initializeClass(libgcj.so.7rh)
at
uk.ac.bbsrc.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:83)
at
uk.ac.bbsrc.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:113)
at uk.ac.bbsrc.babraham.FastQC.Analysis.OfflineRunner.(OfflineRunner.java:84)
at
uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:308)
Caused by: java.lang.ClassFormatError: org.itadaki.bzip2.BZip2InputStream
(unrecognized class file version)
at java.lang.VMClassLoader.defineClass(libgcj.so.7rh)
at java.lang.ClassLoader.defineClass(libgcj.so.7rh)
at java.security.SecureClassLoader.defineClass(libgcj.so.7rh)
at java.net.URLClassLoader.findClass(libgcj.so.7rh)
at java.lang.ClassLoader.loadClass(libgcj.so.7rh)
at java.lang.ClassLoader.loadClass(libgcj.so.7rh)
at java.lang.Class.forName(libgcj.so.7rh)
at java.lang.Class.initializeClass(libgcj.so.7rh)
...4 more

Any clues/advice most appreciated!

Todd

--
*
Todd Oakley, Professor
Ecology Evolution and Marine Biology
University of California, Santa Barbara
Santa Barbara, CA 93106 USA

NEWLY UPDATED LAB WEBSITE:http://labs.eemb.ucsb.edu/oakley/todd/
**

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Re: [galaxy-dev] fastqc in local galaxy - problem