Re: [galaxy-dev] Papers that cite Galaxy workflows

[Steve Cassidy]

Thanks Dave, that’s just what I’m looking for, I found a few good examples of 
workflow citations.

Steve

—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

On 27 Jul 2016, at 6:29 AM, Dave Clements 
> wrote:

Hi Steve,

I don't have a precise answer to your question, but the Galaxy CiteULike 
archive might be helpful here.  Any paper that uses, extends, or references 
Galaxy gets put in that library.  Papers are tagged with one or more of 17 
tags.  There aren't specific tags for 
"defines and publishes a workflow" or "reuses a previously published workflow" 
but I'm pretty sure I've come across many papers that do this.

A good place to start though would be papers with the shared 
tag: Papers that have 
published/shared workflows, histories, datasets, pages, visualizations in a 
Galaxy instance.

Also, not sure if 
CloudMap qualifies here, 
but if it does, many papers that reference it are reusing the pipeline defined 
in it.

Hope this helps,

Dave C

On Thu, Jul 21, 2016 at 7:21 PM, Steve Cassidy 
> wrote:
Hi all,
 I’m writing a paper that will include some evangelism for Galaxy in language 
sciences and I’d like to be able to cite examples of papers in the Bio field 
that cite Galaxy workflows.  Even better would be the re-use of a Galaxy 
workflow cited in another paper.  Does anyone have any good example papers they 
could refer me to.

Thanks,

Steve
—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy


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Re: [galaxy-dev] DOS attack launched from our Galaxy instance

[Suderman Keith]

Hi Dannon,

No, I never did figure out what happened.  I couldn't find anything in our log 
files and Incapsula wasn't very helpful.  Since it was just a 
testing/development instance I simply took it down and spun up a new instance 
with better security/passwords as I did have two Tomcat instances also running 
with relatively weak passwords.  There hasn't been any problem since.

Keith

> On Jul 25, 2016, at 9:51 AM, Dannon Baker  wrote:
> 
> Keith,
> 
> Did you figure this out?  I'm very curious as to what this was.  Outside mass 
> admin tool updates, or maybe wheel installation, I can't think of anything 
> that would have triggered anything like this on the Galaxy side.
> 
> -Dannon
> 
> On Wed, Jul 13, 2016 at 5:31 PM Suderman Keith  > wrote:
> We are in the process of installing a Galaxy instance to Amazon EC2 and this 
> morning I received an email from ec2-ab...@amazon.com 
>  saying that our EC2 instance has been flooding 
> 45.64.64.40 with data in what looks like a DOS attack. A whois shows that the 
> IP belongs to Incapsula, which appears to be a load balancing proxy server.  
> Does anyone here recognize the IP or use Incapsula?  My first thought is that 
> something in Galaxy might be trying to "phone home".
> 
> The Galaxy instance we are using is based on the galaxy-stable:16.04 Docker 
> image from Björn with a few of our tools installed for testing. I've locked 
> down access to the instance until I figure out what happened and I wanted to 
> check in here first to see if I’ve been DOS’ing the Galaxy infrastructure or 
> if anyone recognizes the IP address.
> 
> Keith
> 
> --
> Research Associate
> Department of Computer Science
> Vassar College
> Poughkeepsie, NY
> 
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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> 
--
Research Associate
Department of Computer Science
Vassar College
Poughkeepsie, NY



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Re: [galaxy-dev] Galaxy Blast

[Daniel Blankenberg]

Hi Peter and Harry,

When a tool is installed from the toolshed, the tool data table loc files are 
installed to the configured location and are then referenced in 
shed_tool_data_table_conf.xml. You should be able to modify the .loc files as 
referenced in this file, or, as you did, add a new entry to the 
tool_data_table_conf.xml file. Each instance of the tool data table (one will 
exist per tool shed repository revision that has been installed) will be merged 
together into a single entity that can then be accessed by the tools. You can 
also find the paths to the .loc files for each tool data table under the admin 
interface. Data Managers will write to the specific .loc file that was created 
during their installation.

Please let me know if I can provide additional clarification. 



Thanks for using Galaxy,

Dan


> On Jul 26, 2016, at 6:08 AM, Peter Cock  wrote:
> 
> Hello all,
> 
> Harry (CC'd) emailed me about some teething trouble getting
> nucleotide BLAST databases to appear in the drop down lists
> (see below).
> 
> I suspect this is partly due to the partial data table sample that
> ships with Galaxy:
> 
> https://github.com/galaxyproject/galaxy/blob/dev/config/tool_data_table_conf.xml.sample
> 
> Can any of the Galaxy Data Manager expects advise please?
> 
> Thanks,
> 
> Peter
> 
> 
> -- Forwarded message --
> From: Harry Wright 
> Date: Tue, Jul 26, 2016 at 9:25 AM
> Subject: RE: Galaxy Blast
> To: Peter Cock 
> 
> 
> Hi Peter,
> 
> Sorry for the delay in response. If you think it would be useful please post 
> it.
> 
> I have downloaded what I thought was the newest versions of NCIB
> blast+ 2.2.31 from the toolshed.
> 
> The tool_data_table_conf.xml.sample I altered was in galaxy_dir/config/.
> 
> If you need anything else please ask.
> 
> Thanks
> Harry
> 
> -Original Message-
> From: Peter Cock [mailto:p.j.a.c...@googlemail.com]
> Sent: 22 July 2016 16:28
> To: Harry Wright
> Subject: Re: Galaxy Blast
> 
> Hi Harry,
> 
> Hmm. I'm a little puzzled. That file looks fine on our GitHub and on
> the Tool Shed:
> 
> https://github.com/peterjc/galaxy_blast/blob/master/tool-data/tool_data_table_conf.xml.sample
> 
> http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus (browse tip files)
> 
> Can you tell me exactly which version of things you got from the Tool
> Shed, and exactly which tool_data_table_conf.xml and
> tool_data_table_conf.xml.sample you had to edit?
> 
> My guess is the problem is this partial example that ships with Galaxy:
> 
> https://github.com/galaxyproject/galaxy/blob/dev/config/tool_data_table_conf.xml.sample
> 
> (There is talk of moving datatypes like this back into the Galaxy
> core, which would simply this)
> 
> May I forward this email to the public Galaxy developers mailing list please?
> 
> Thanks,
> 
> Peter
> 
> On Fri, Jul 22, 2016 at 3:59 PM, Harry Wright
>  wrote:
>> 
>> 
>> Dear Peter,
>> 
>> 
>> 
>> I have just installed a new instance of Galaxy here at Moredun and
>> have been busy setting up tools for us to use. One of the tools that I
>> have set up is blast with the NCBI nr and nt databases sitting in the
>> backend as a Locally installed database. I downloaded both files and
>> formatted them into databases. I then add lines to the blastdb_p.loc
>> and blastdb.loc. When I restarted the server I found that I could
>> access nr through the interface, for blastx, but not nt, using blastn.
>> For nt I was getting the message “No option available” in the
>> Nucleotide BLAST database drop down when I selected “Locally installed BLAST 
>> database”.
>> 
>> 
>> 
>> After some searching I found reference to
>> config/tool_data_table_conf.xml.sample. When I look there I could only
>> find reference to blastdb_p and not blastdb.
>> 
>> 
>> 
>> I added the lines below to the file and changed the file name to
>> tool_data_table_conf.xml. I  restarted galaxy to find that I could now
>> use nt in blastn.
>> 
>> 
>> 
>> 
>> 
>>
>> 
>>value, name, path
>> 
>>
>> 
>>
>> 
>> 
>> 
>> I was wondering if there was something that I have missed or has this
>> section of the code been missed out of the tool_data_table_conf.xml
>> file in the installation download?
>> 
>> 
>> 
>> Regards
>> 
>> Harry
>> 
>> 
>> 
>> Dr. Harry Wright
>> 
>> Moredun Research Institute
>> 
>> Pentlands Science Park
>> 
>> Bush Loan
>> 
>> Penicuik
>> 
>> Midlothian EH26 0PZ
>> 
>> Tel - 0131 4455111
>> 
>> Fax - 0131 4456235
>> 
>> 
>> 
>> The Moredun Research Institute is a limited company registered in Scotland.
>> Registered number: SC149440
>> 
>> The Moredun Research Institute is a charity registered in Scotland.
>> Registered number: SC022353
>> 
>> Registered office: Moredun Research Institute, Pentlands Science Park,
>> Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK
>> 
>> 
> 
> 
> 
> The Moredun Research Institute is a limited 

Re: [galaxy-dev] Papers that cite Galaxy workflows

[Dave Clements]

Hi Steve,

I don't have a precise answer to your question, but the Galaxy CiteULike
archive might be helpful here.  Any paper that uses, extends, or references
Galaxy gets put in that library.  Papers are tagged with one or more of 17
tags .  There aren't specific
tags for "defines and publishes a workflow" or "reuses a previously
published workflow" but I'm pretty sure I've come across many papers that
do this.

A good place to start though would be papers with the shared tag
: Papers that have
published/shared workflows, histories, datasets, pages, visualizations in a
Galaxy instance.

Also, not sure if CloudMap
 qualifies here, but
if it does, many papers that reference it are reusing the pipeline defined
in it.

Hope this helps,

Dave C

On Thu, Jul 21, 2016 at 7:21 PM, Steve Cassidy 
wrote:

> Hi all,
>  I’m writing a paper that will include some evangelism for Galaxy in
> language sciences and I’d like to be able to cite examples of papers in the
> Bio field that cite Galaxy workflows.  Even better would be the re-use of a
> Galaxy workflow cited in another paper.  Does anyone have any good example
> papers they could refer me to.
>
> Thanks,
>
> Steve
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>



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http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/
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[galaxy-dev] Fwd: Immersive Approaches to Biological Data Visualization CSHL Course December 2016

[James Taylor]

Hello all,

As many of you are interested in visualization I wanted to draw your
attention to this NEW course on biological data visualization at Cold
Spring Harbor, which is being led by some of our colleagues at the Texas
Advanced Computing Center (who provide substantial support for Galaxy
main). It will be very interesting to think about how immersive
visualizations can be implemented in Galaxy in the future.

-- jt

-- Forwarded message --
From: Cold Spring Harbor Laboratory 
Date: Tue, Jul 12, 2016 at 9:02 AM
Subject: Immersive Approaches to Biological Data Visualization CSHL Course
December 2016
To: ja...@jamestaylor.org




Immersive Approaches to Biological Data Visualization

December 1 - 10, 2016
*Applications due: August 15*
*Instructors*

*Kelly Gaither,* Texas Advanced Computing Center
*Matthew Vaughn,* Texas Advanced Computing Center

This course will explore the new frontier of immersive, interactive
scientific visualization. It is aimed at researchers who wish to design and
implement innovative visualization tools to help address biological or
biomedical research questions. As part of their research programs, course
participants will ideally have a need to visualize genomic or systems
biology data, anatomical structures and models, scientific simulations,
and/or other domains that generate complex, multidimensional, and often
very large data sets.

Through a combination of detailed lectures and intensive hands-on computing
exercises led by course instructors, students will learn the principles of
information and scientific visualization. However, rather than relying on
simplified representations of complex data, students will learn these
visualization principles within the newly emerging context of immersive
augmented and virtual reality. They will work with tools such as Unity 3D
and Blender, as well as scripting environments such as Bash and Python, to
craft data visualizations using the Oculus Rift

virtual reality headset and Leap Motion

gesture sensor. Students will apply the concepts and techniques covered in
class exercises to create an independent virtual reality data visualization
project. Additionally, the hands-on training will be supplemented by guest
lectures from some of the leading experts working in data visualization
today.

*Selected Major Topics*

   - Overview of Scientific Visualization
   - Perception & Color
   - Information Visualization
   - Scientific Visualization
   - Importing Scientific Data into an Immersive Visualization Framework
   - Tool Development Using Oculus and Leap Motion

*Invited Speakers*

*Min Chen,* Oxford University, U.K.
*David Ebert,* Purdue University School of Electrical & Computer Engineering
*Robert Kosara,* Tableau Software, Inc.
*Brian McCann,* Texas Advanced Computing Center
*Mariah Meyer,* University of Utah
*Hanspeter Pfister,* Harvard University School of Engineering & Applied
Sciences
*Amitabh Varshney,* University of Maryland College Park

Please click this link to go to the Immersive Approaches to Biological Data
Visualization course website for more info.

Re: [galaxy-dev] Consuming dataset collections

[John Chilton]

Thanks for the questions - I have tried to revise the planemo docs to
be more explicit about what collection identifiers are and where they
come from 
(https://github.com/galaxyproject/planemo/commit/a811e652f23d31682f862f858dc792c1ef5a99ce).
http://planemo.readthedocs.io/en/latest/writing_advanced.html#collections

I think this might be a case where I'm too close the problem - I
implemented collections, the tooling around them, and planemo docs so
there is probably a lot that I just assume is implicit when it is
completely non-obvious.

The collection identifier in your case is going to be something like:
1_1308_1_2_092-ch6-speaker16. The designation in the previous step -
the outputing a collection with discovered datasets - if it is
producing a collection should actually be called "identifier". The
terms "desigination" and "identifier" are inter-changable from a
Galaxy perspective - but I prefer using the term "identifier" for
collections and the older "desigination" when discovered un-collected
individual datasets.

There was a little warning explaining the odd whitespace replacement
stuff that got shifted around at some point in the planemo docs - I
think I have corrected that now. The explanation for fixing up the
identifier was this:

"Here we are rewriting the element identifiers to assure everything is
safe to put on the command-line. In the future, collections will not
be able to contain keys that are potentially harmful and this won't be
necessary."

So yes this is the name you are after.

As for the quesstion, "Is a manifest-based approach a silly idea?" -
not at all, not in the least. I'd prefer to have both options
available - this current option is nice because it doesn't require a
"wrapper" script - you can build command lines and such from the
cheetah template - but definitely people already working with and
thinking about collections from inside some sort of script should have
the option to consume and produce manifests of files.

I've created an issue for this idea here -
https://github.com/galaxyproject/galaxy/issues/2658. I'm not sure if
I'll have time to get to it anytime soon - but if you or someone else
is eager to tackle the problem I could scope out an implementation
plan for this.

Thanks for the e-mail and I hope this helps,

-John

On Tue, Jul 26, 2016 at 1:59 AM, Steve Cassidy  wrote:
> Hi all,
>I’m staring at the discussion of handling dataset collections:
>
> http://planemo.readthedocs.io/en/latest/_writing_collections.html
>
> but failing to see the solution to my problem.
>
> I have a tool that creates a dataset collection, a group of files with names
> like 1_1308_1_2_092-ch6-speaker16.TextGrid where the 1_1308_1_2_092 part is
> a unique identifier that I’d like to keep track of.  I’ve used a
> discover_datasets tag in the tool xml file to match my output filenames and
> extract the designation (1_1308_1_2_092-ch6-speaker16.TextGrid) and the ext
> (TextGrid).
>
> I have another tool that runs a query over these files and generates a
> single tabular result that will ideally include the identifier in some form.
> Here’s the command section for that tool:
>
> query_textgrids.py --textgrid "${",".join(map(str, $textgrid))}"
> --tier $tier --regex '$regex' --output_path $output
>
> where ‘$textgrid’ is one of my input parameters that has multiple=“true” set
> so that it can be a dataset collection.  That works ok but the input I get
> are the filenames (dataset_1.dat, etc.) not the name of the datasets.
>
> The page above mentions something called the ‘element_identifier’ and gives
> this funky example:
>
> merge_rows --name "${re.sub('[^\w\-_]', '_', $input.element_identifier)}"
> --file "$input" --to $output;
>
> I can’t see what this element_identifier thing is - the suggestion is that
> it might be the dataset name, but I’m not sure.  Also I don’t understand why
> the command above is doing replacement of whitespace with underscores.
>
> If this is the name I’m after, it would seem that I’d need to pass these
> names along with the textgrid files and then pair them up inside my script -
> is that what I need to do?
>
> All of this cries out to me for a more explicit representation of a dataset
> collection that my tool can create and consume rather than this hacky
> treatment of filenames.   If I could generate a manifest file of some kind
> describing my dataset collection then none of this parsing of filenames
> would be needed.  I could also consume the manifest file as well and it
> could be used for collection level metadata.  Is this a silly idea?
>
> Anyway, any help with my immediate problem would be appreciated.
>
> Thanks,
>
> Steve
>
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other 

[galaxy-dev] Fwd: Galaxy Blast

[Peter Cock]

Hello all,

Harry (CC'd) emailed me about some teething trouble getting
nucleotide BLAST databases to appear in the drop down lists
(see below).

I suspect this is partly due to the partial data table sample that
ships with Galaxy:

https://github.com/galaxyproject/galaxy/blob/dev/config/tool_data_table_conf.xml.sample

Can any of the Galaxy Data Manager expects advise please?

Thanks,

Peter


-- Forwarded message --
From: Harry Wright 
Date: Tue, Jul 26, 2016 at 9:25 AM
Subject: RE: Galaxy Blast
To: Peter Cock 


Hi Peter,

Sorry for the delay in response. If you think it would be useful please post it.

I have downloaded what I thought was the newest versions of NCIB
blast+ 2.2.31 from the toolshed.

The tool_data_table_conf.xml.sample I altered was in galaxy_dir/config/.

If you need anything else please ask.

Thanks
Harry

-Original Message-
From: Peter Cock [mailto:p.j.a.c...@googlemail.com]
Sent: 22 July 2016 16:28
To: Harry Wright
Subject: Re: Galaxy Blast

Hi Harry,

Hmm. I'm a little puzzled. That file looks fine on our GitHub and on
the Tool Shed:

https://github.com/peterjc/galaxy_blast/blob/master/tool-data/tool_data_table_conf.xml.sample

http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus (browse tip files)

Can you tell me exactly which version of things you got from the Tool
Shed, and exactly which tool_data_table_conf.xml and
tool_data_table_conf.xml.sample you had to edit?

My guess is the problem is this partial example that ships with Galaxy:

https://github.com/galaxyproject/galaxy/blob/dev/config/tool_data_table_conf.xml.sample

(There is talk of moving datatypes like this back into the Galaxy
core, which would simply this)

May I forward this email to the public Galaxy developers mailing list please?

Thanks,

Peter

On Fri, Jul 22, 2016 at 3:59 PM, Harry Wright
 wrote:
>
>
> Dear Peter,
>
>
>
> I have just installed a new instance of Galaxy here at Moredun and
> have been busy setting up tools for us to use. One of the tools that I
> have set up is blast with the NCBI nr and nt databases sitting in the
> backend as a Locally installed database. I downloaded both files and
> formatted them into databases. I then add lines to the blastdb_p.loc
> and blastdb.loc. When I restarted the server I found that I could
> access nr through the interface, for blastx, but not nt, using blastn.
> For nt I was getting the message “No option available” in the
> Nucleotide BLAST database drop down when I selected “Locally installed BLAST 
> database”.
>
>
>
> After some searching I found reference to
> config/tool_data_table_conf.xml.sample. When I look there I could only
> find reference to blastdb_p and not blastdb.
>
>
>
> I added the lines below to the file and changed the file name to
> tool_data_table_conf.xml. I  restarted galaxy to find that I could now
> use nt in blastn.
>
>
>
> 
>
> 
>
> value, name, path
>
> 
>
> 
>
>
>
> I was wondering if there was something that I have missed or has this
> section of the code been missed out of the tool_data_table_conf.xml
> file in the installation download?
>
>
>
> Regards
>
> Harry
>
>
>
> Dr. Harry Wright
>
> Moredun Research Institute
>
> Pentlands Science Park
>
> Bush Loan
>
> Penicuik
>
> Midlothian EH26 0PZ
>
> Tel - 0131 4455111
>
> Fax - 0131 4456235
>
>
>
> The Moredun Research Institute is a limited company registered in Scotland.
> Registered number: SC149440
>
> The Moredun Research Institute is a charity registered in Scotland.
> Registered number: SC022353
>
> Registered office: Moredun Research Institute, Pentlands Science Park,
> Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK
>
>



The Moredun Research Institute is a limited company registered
in Scotland. Registered number: SC149440

The Moredun Research Institute is a charity registered in
Scotland. Registered number: SC022353

Registered office: Moredun Research Institue, Pentlands
Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK
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Re: [galaxy-dev] This job failed for reasons that could not be determined.

[Ulf Schaefer]

Hi Hans-Rudolf

It happens with a number of tools. I will need to do some more testing 
to see if I can narrow it down further.

Thanks for your help
Ulf



On 26/07/16 07:13, Hans-Rudolf Hotz wrote:
> Hi Ulf
>
>
> I don't think the two things are connected which each other. In the logs
> of our local installation we see once in a while, lines like:
>
>
>   File "/usr/lib64/python2.6/socket.py", line 303, in flush
> self._sock.sendall(buffer(data, write_offset, buffer_size))
> error: [Errno 32] Broken pipe
>
> but without any errors or failed jobs associated. We consider those as
> harmless, temporary glitches in the web server part of galaxy.
>
> Sorry, not much help...
>
>
> Just one question for clarification, which might help others (with more
> cloud experience) to jump in: do the failed jobs occur randomly with any
> tool? or are they all coming from the same tool?
>
>
> Regards, Hans-Rudolf
>
>
>
>
> On 07/25/2016 12:48 PM, Ulf Schaefer wrote:
>> Hi all
>>
>> Certain jobs fail on my cloud Galaxy instance with the error message in
>> the subject line. No stderr or stdout is produced by the tool, at least
>> it's not accessible from Galaxy. However the data seems to be there, in
>> so far that I can view it (clicking on the eye) and download it using
>> the floppy disk icon.
>>
>> The only thing I see (repeatedly) in my Galaxy logs is this:
>>
>> 
>> Exception happened during processing of request from ('127.0.0.1', 46619)
>> Traceback (most recent call last):
>>  File
>> "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
>>
>> line 1085, in process_request_in_thread
>>self.finish_request(request, client_address)
>>  File "/usr/lib/python2.7/SocketServer.py", line 334, in
>> finish_request
>>self.RequestHandlerClass(request, client_address, self)
>>  File "/usr/lib/python2.7/SocketServer.py", line 657, in __init__
>>self.finish()
>>  File "/usr/lib/python2.7/SocketServer.py", line 716, in finish
>>self.wfile.close()
>>  File "/usr/lib/python2.7/socket.py", line 283, in close
>>self.flush()
>>  File "/usr/lib/python2.7/socket.py", line 307, in flush
>>self._sock.sendall(view[write_offset:write_offset+buffer_size])
>> error: [Errno 32] Broken pipe
>> 
>>
>> Does this look familiar to anyone?
>>
>> Thanks very much for any input
>> Ulf
>>
>> **
>>
>> The information contained in the EMail and any attachments is
>> confidential and intended solely and for the attention and use of the
>> named addressee(s). It may not be disclosed to any other person
>> without the express authority of Public Health England, or the
>> intended recipient, or both. If you are not the intended recipient,
>> you must not disclose, copy, distribute or retain this message or any
>> part of it. This footnote also confirms that this EMail has been swept
>> for computer viruses by Symantec.Cloud, but please re-sweep any
>> attachments before opening or saving. http://www.gov.uk/PHE
>> **
>>
>> ___
>> Please keep all replies on the list by using "reply all"
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>>

**
The information contained in the EMail and any attachments is confidential and 
intended solely and for the attention and use of the named addressee(s). It may 
not be disclosed to any other person without the express authority of Public 
Health England, or the intended recipient, or both. If you are not the intended 
recipient, you must not disclose, copy, distribute or retain this message or 
any part of it. This footnote also confirms that this EMail has been swept for 
computer viruses by Symantec.Cloud, but please re-sweep any attachments before 
opening or saving. http://www.gov.uk/PHE
**
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/