Re: [galaxy-dev] using tags with regular expressions or mathematical expressions...

[Nikhil Joshi]

So I figured it out... but for those who need to know:  You can put the
expression (e.g. value % 2 == 0) or the regex between the validator tags.  I
guess you have to use the keyword "value" for a mathematical  expression or
a regex to access the value of the field.  So my validator for checking if
the number was even looked like this:

value % 2 ==
0

- Nik.

On Tue, Aug 9, 2011 at 5:47 PM, Nikhil Joshi
wrote:

> Hi all,
>
> I would like to use the validator tag to validate data using either regexes
> or math expressions.  How can I do this?  I tried using the "regex" type,
> but I'm not sure where to put the regex itself.  I tried putting it in a
> file that was in the filename attribute, but that didn't seem to work.
> Essentially, I want to check if an integer input is even or not.
>
> - Nik.
>
> --
> Nikhil Joshi
> Bioinformatics Programmer
> UC Davis Genome Center
> University of California, Davis
> Davis, CA
> http://bioinformatics.ucdavis.edu
>



-- 
Nikhil Joshi
Bioinformatics Programmer
UC Davis Genome Center
University of California, Davis
Davis, CA
http://bioinformatics.ucdavis.edu
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[galaxy-dev] using tags with regular expressions or mathematical expressions...

[Nikhil Joshi]

Hi all,

I would like to use the validator tag to validate data using either regexes
or math expressions.  How can I do this?  I tried using the "regex" type,
but I'm not sure where to put the regex itself.  I tried putting it in a
file that was in the filename attribute, but that didn't seem to work.
Essentially, I want to check if an integer input is even or not.

- Nik.

-- 
Nikhil Joshi
Bioinformatics Programmer
UC Davis Genome Center
University of California, Davis
Davis, CA
http://bioinformatics.ucdavis.edu
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Re: [galaxy-dev] Customizing/reusing the workflows/run.mako template

[James Taylor]

John, the prefixes like "22|" are added to the inputs associated with each 
step, so that they can be separated back out. In this case, the chunk of HTML 
you have pasted likely corresponds to the 22nd step of the workflow. 

53 on the other hand should be a dataset id from the current history (unencoded 
in this case).

On Aug 9, 2011, at 8:24 PM, Duddy, John wrote:

> I’d like to integrate with Galaxy and launch workflows, and I am hoping to 
> reuse  Galaxy’s support for prompting the user for items that are tagged as 
> being set at runtime. It looks to me that I could load the workflows/run page 
> in a frame on my app (on the same server) and reuse it.
>  
> The problem I’m having is that I don’t understand how the parameters for the 
> input files are encoded. For example, here is one for adding a column to a 
> dataset:
> 
> 1: Add column on data 6
> 
> 
> 
> 
> 
> What are 22 and 53? They don’t seem to correspond to dataset IDs.
>  
> Is there a way that I can encode data library IDs such that I can submit this 
> form and have Galaxy run the workflow with the right files in a new history?
>  
> Thanks!
>  
> John Duddy
> Sr. Staff Software Engineer
> Illumina, Inc.
> 9885 Towne Centre Drive
> San Diego, CA 92121
> Tel: 858-736-3584
> E-mail: jdu...@illumina.com
>  
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[galaxy-dev] Customizing/reusing the workflows/run.mako template

[Duddy, John]

I'd like to integrate with Galaxy and launch workflows, and I am hoping to 
reuse  Galaxy's support for prompting the user for items that are tagged as 
being set at runtime. It looks to me that I could load the workflows/run page 
in a frame on my app (on the same server) and reuse it.

The problem I'm having is that I don't understand how the parameters for the 
input files are encoded. For example, here is one for adding a column to a 
dataset:








1: Add column on data 6
















What are 22 and 53? They don't seem to correspond to dataset IDs.

Is there a way that I can encode data library IDs such that I can submit this 
form and have Galaxy run the workflow with the right files in a new history?

Thanks!

John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Tel: 858-736-3584
E-mail: jdu...@illumina.com

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Re: [galaxy-dev] syntax and #if and #for statements within the tag

[Dannon Baker]

Nik,

The syntax is Cheetah, (http://www.cheetahtemplate.org/).  Also, see more about 
some of the extra tags available on the galaxy wiki, 
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Ccommand.3E_tag_set

-Dannon


On Aug 9, 2011, at 6:29 PM, Nikhil Joshi wrote:

> Hi all,
> 
> So I've gotten some simple custom tools to work on our local Galaxy, however, 
> I am having trouble figuring out exactly how the syntax works for the 
> commands and lines within the  tag.  E.g., I've seen #if and #for 
> statements and also lines using functions like "str", but I can't really find 
> any documentation about exactly how the syntax works.  It kinda seems like 
> PHP syntax, but not quite?  Anyways, any help would be highly appreciated.  
> Thanks!
> 
> - Nik.
> 
> 
> On Wed, Aug 3, 2011 at 6:20 AM, Greg Von Kuster  wrote:
> Hello Nikhil,
> 
> I am responsible for the tool shed ( both implementation as well as 
> documentation ), and finally got a chance to get the wiki started yesterday 
> (that's why it is currently lacking in information).  I will be working on 
> the wiki as the top priority now, so it should be fairly useful within the 
> next day or so.  In the meantime, please feel free to direct any questions to 
> the mail list, and I'll answer them in short order.
> 
> Getting started with the tool shed is fairly straight-forward.  You can 
> browse existing repositories to see how others have designed their file 
> hierarchies.  Many very good examples of repositories have been created by 
> Peter Cock ( his public username on the tool shed is peterjc ), so browse 
> some of his repositories to get an idea.  Here's a good example of a repo 
> that includes a single tool that uses a .loc file:
> 
> Contents:
> effectivet3
> tool-data/
> effectiveT3.loc.sample
> tools/
> protein_analysis/
> effectiveT3.py
> effectiveT3.txt
> effectiveT3.xml
> 
> 
> You can browse repos without authenticating, but in order to create a repo, 
> you'll need to authenticate, so create an account on the tool shed if you 
> don't yet have one.
> 
> Regarding your questions about the "XML format for the XML file", the 
> repository is simply a container for files of any type ( tool configs, data, 
> binaries, python scripts, exported Galaxy workflows, etc ), so the repository 
> itself has no requirement for XML formats, etc.  Generally, XML files will 
> simply be the Galaxy tool config, the syntax of which is defined on our wiki 
> at http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax
> 
> Thanks very much for you interest in the tool shed,
> 
> Greg Von Kuster
> 
> 
> On Aug 2, 2011, at 10:36 PM, Nikhil Joshi wrote:
> 
>> Hi all,
>> 
>> I have been using Galaxy for a few years now and I am about to start 
>> creating my own repositories for the new Tool Shed.  However, I can't seem 
>> to find any good documentation on how to do that exactly.  Can someone point 
>> me in the right direction?  I need to figure out the best way to organize a 
>> repository, the XML format for the XML file, and any other important things 
>> that I might need to know?  Is there a good resource for all that?  The wiki 
>> has a section entitled "Create a new repository", but there is nothing in 
>> it.  Any help would highly appreciated.  Thanks!
>> 
>> - Nik.
>> 
>> -- 
>> Nikhil Joshi
>> Bioinformatics Programmer
>> UC Davis Genome Center
>> University of California, Davis
>> Davis, CA
>> http://bioinformatics.ucdavis.edu
>> ___
>> 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:
>> 
>>  http://lists.bx.psu.edu/
> 
> Greg Von Kuster
> Galaxy Development Team
> g...@bx.psu.edu
> 
> 
> 
> 
> 
> 
> -- 
> Nikhil Joshi
> Bioinformatics Programmer
> UC Davis Genome Center
> University of California, Davis
> Davis, CA
> http://bioinformatics.ucdavis.edu
> ___
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Re: [galaxy-dev] Failure to prepare job error

[Enis Afgan]

Hi Rafi,
Based on the error report, it looks like a problem with the template. Is the
tool form rendering in the browser and the job is failing once you hit
submit job or earlier?
Also, running from the command line that works - this is on the same amazon
instance or your local instance?
Lastly, the path that keeps showing up (/nfs/sftware...) - is this something
you have added and configured on your amazon instance or is this left over
from your local deployment?

Enis

On Mon, Aug 1, 2011 at 1:38 AM, Faiaz Khan  wrote:

> Hello,
>
> I'm running a Python/R tool from my Amazon Galaxy instance. To use R, I
> import a package I've installed called PypeR. My tool works fine from the
> command line, but when I try to run it on my Amazon instance, it gives me
> this error:
>
> Traceback (most recent call last):
>   File "/nfs/software/galaxy/lib/galaxy/jobs/runners/local.py", line 61, in 
> run_job
> job_wrapper.prepare()
>   File "/nfs/software/galaxy/lib/galaxy/jobs/__init__.py", line 371, in 
> prepare
> self.command_line = self.tool.build_command_line( param_dict )
>   File "/nfs/software/galaxy/lib/galaxy/tools/__init__.py", line 1543, in 
> build_command_line
> command_line = fill_template( self.command, context=param_dict )
>   File "/nfs/software/galaxy/lib/galaxy/util/template.py", line 9, in 
> fill_template
> return str( Template( source=template_text, searchList=[context] ) )
>   File 
> "/nfs/software/galaxy/eggs/Cheetah-2.2.2-py2.6-linux-i686-ucs4.egg/Cheetah/Template.py",
>  line 1004, in __str__
> return getattr(self, mainMethName)()
>   File "cheetah_DynamicallyCompiledCheetahTemplate_1311891781_86_41894.py", 
> line 83, in respond
> EOFError: EOF when reading a line
>
> With the additional caption "failure to prepare job".
> I've been struggling with this for days, and I'm pretty sure I don't have a 
> typo in my .xml file. How can I solve this?
>
>
> Thanks,
>
> Rafi
>
>
>
>
>
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>
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[galaxy-dev] syntax and #if and #for statements within the tag

[Nikhil Joshi]

Hi all,

So I've gotten some simple custom tools to work on our local Galaxy,
however, I am having trouble figuring out exactly how the syntax works for
the commands and lines within the  tag.  E.g., I've seen #if and
#for statements and also lines using functions like "str", but I can't
really find any documentation about exactly how the syntax works.  It kinda
seems like PHP syntax, but not quite?  Anyways, any help would be highly
appreciated.  Thanks!

- Nik.


On Wed, Aug 3, 2011 at 6:20 AM, Greg Von Kuster  wrote:

> Hello Nikhil,
>
> I am responsible for the tool shed ( both implementation as well as
> documentation ), and finally got a chance to get the wiki started yesterday
> (that's why it is currently lacking in information).  I will be working on
> the wiki as the top priority now, so it should be fairly useful within the
> next day or so.  In the meantime, please feel free to direct any questions
> to the mail list, and I'll answer them in short order.
>
> Getting started with the tool shed is fairly straight-forward.  You can
> browse existing repositories to see how others have designed their file
> hierarchies.  Many very good examples of repositories have been created by
> Peter Cock ( his public username on the tool shed is peterjc ), so browse
> some of his repositories to get an idea.  Here's a good example of a repo
> that includes a single tool that uses a .loc file:
>
> Contents:
> effectivet3
> tool-data/
> effectiveT3.loc.sample
> tools/
> protein_analysis/
> effectiveT3.py
> effectiveT3.txt
> effectiveT3.xml
>
>
> You can browse repos without authenticating, but in order to create a repo,
> you'll need to authenticate, so create an account on the tool shed if you
> don't yet have one.
>
> Regarding your questions about the "XML format for the XML file", the
> repository is simply a container for files of any type ( tool configs, data,
> binaries, python scripts, exported Galaxy workflows, etc ), so the
> repository itself has no requirement for XML formats, etc.  Generally, XML
> files will simply be the Galaxy tool config, the syntax of which is defined
> on our wiki at
> http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax
>
> Thanks very much for you interest in the tool shed,
>
> Greg Von Kuster
>
>
> On Aug 2, 2011, at 10:36 PM, Nikhil Joshi wrote:
>
> Hi all,
>
> I have been using Galaxy for a few years now and I am about to start
> creating my own repositories for the new Tool Shed.  However, I can't seem
> to find any good documentation on how to do that exactly.  Can someone point
> me in the right direction?  I need to figure out the best way to organize a
> repository, the XML format for the XML file, and any other important things
> that I might need to know?  Is there a good resource for all that?  The wiki
> has a section entitled "Create a new repository", but there is nothing in
> it.  Any help would highly appreciated.  Thanks!
>
> - Nik.
>
> --
> Nikhil Joshi
> Bioinformatics Programmer
> UC Davis Genome Center
> University of California, Davis
> Davis, CA
> http://bioinformatics.ucdavis.edu
> ___
> 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:
>
>  http://lists.bx.psu.edu/
>
>
> Greg Von Kuster
> Galaxy Development Team
> g...@bx.psu.edu
>
>
>
>


-- 
Nikhil Joshi
Bioinformatics Programmer
UC Davis Genome Center
University of California, Davis
Davis, CA
http://bioinformatics.ucdavis.edu
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[galaxy-dev] cant' run galaxy in daemon mode

[sohkhan]

Hi,
I have the production Galaxy setup and running on Mac OS Leopard 10.6, 
with postgres and apache.  However, I am unable to run it as daemon.  I 
don't get an error, the browser just hangs there.
Thanks for any advice.

-Sohail
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Re: [galaxy-dev] invalid password

[sohkhan]

Hi Jennifer,
Problem solved!
I hadn't registered through UI.
Thanks for your help.
-Sohail



From:   Jennifer Jackson 
To: sohk...@notes.cc.sunysb.edu
Cc: galaxy-dev@lists.bx.psu.edu
Date:   08/09/2011 02:48 PM
Subject:Re: [galaxy-dev] invalid password



Hello Sohail,

The universe_wsgi.ini for admin is correct. Have you registered through 
the UI yet? Once registered and logged in with these same credentials, 
the account should be granted admin permissions.

Jen

On 8/9/11 11:25 AM, sohk...@notes.cc.sunysb.edu wrote:
> Thanks Jennifer,
> I login with my e-mail,I have admin_users=my_email and
> admin_pass=my_password setup in universe_wsgi.ini. However, I am not
> sure if this correct. What is the admin password when you login for the
> first time?
> -Sohail
>
>
>
> From: Jennifer Jackson 
> To: sohk...@notes.cc.sunysb.edu
> Cc: galaxy-dev@lists.bx.psu.edu
> Date: 08/09/2011 02:11 PM
> Subject: Re: [galaxy-dev] invalid password
> 
>
>
>
> Hello Sohail,
>
> Just as a start, if you have already followed the production server set
> up procedures, double check that you are using the email address (and
> not the user name) when logging into the UI form.
>
> If that does not solve the admin login issue, is likely that you need to
> do some more configuration in the universe_wsgi.ini file. Please see the
> sample in your download or at:
> 
http://bitbucket.org/galaxy/galaxy-central/src/1291bc31fec6/universe_wsgi.ini.sample

>
> In particular, this section in universe_wsgi.ini will need to be set up:
> # -- Users and Security
>
> Start here:
> http://galaxyproject.org/Admin/GetGalaxy
>
> Then see:
> http://galaxyproject.org/Admin/Interface
> http://galaxyproject.org/Admin/Config/Performance/Production%20Server
>
> The two menu items that are not functioning are covered in the above
> configuration documentation or the universe_wsgi.ini.sample comments.
>
> Hopefully this helps,
>
> Best,
>
> Jen
> Galaxy team
>
> On 8/5/11 11:41 AM, sohk...@notes.cc.sunysb.edu wrote:
>  > Hi,
>  >
>  > I have the admin user set in universe_wsgi.ini file, but I am unable 
to
>  > login to Galaxy. I get invalid password error.
>  > In addition, "User" and "Help" menu are not functioning.
>  > Thanks for any solution.
>  >
>  > -Sohail
>  >
>  >
>  > ___
>  > 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:
>  >
>  > http://lists.bx.psu.edu/
>
> --
> Jennifer Jackson
> http://usegalaxy.org 
> http://galaxyproject.org/Support
>

-- 
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support

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Re: [galaxy-dev] how is metadata generated

[Jennifer Jackson]

Hello,

Metadata is associated with each dataset based on the datatype when 
loaded into Galaxy (detected or assigned) and other inputs from tools. 
This wiki document explains how tools generate, organize, and use data 
and should help to address your question.


http://galaxyproject.org/Admin/Tools/Tool%20Config%20Syntax

Thanks!

Jen
Galaxy team

On 8/1/11 7:34 PM, KOH Jia Yu Jayce wrote:

Hi

Just wondering how metadata files in
galaxy-dist/database/files/_metadata_files are generated? Are there any
configurations in the xmls that specify these to be generated? Thanks



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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
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Re: [galaxy-dev] invalid password

[sohkhan]

Thanks Jennifer,
I login with my e-mail,I have admin_users=my_email and 
admin_pass=my_password setup in universe_wsgi.ini.  However, I am not sure 
if this correct.  What is the admin password when you login for the first 
time?
-Sohail



From:   Jennifer Jackson 
To: sohk...@notes.cc.sunysb.edu
Cc: galaxy-dev@lists.bx.psu.edu
Date:   08/09/2011 02:11 PM
Subject:Re: [galaxy-dev] invalid password



Hello Sohail,

Just as a start, if you have already followed the production server set 
up procedures, double check that you are using the email address (and 
not the user name) when logging into the UI form.

If that does not solve the admin login issue, is likely that you need to 
do some more configuration in the universe_wsgi.ini file. Please see the 
sample in your download or at:
http://bitbucket.org/galaxy/galaxy-central/src/1291bc31fec6/universe_wsgi.ini.sample


In particular, this section in universe_wsgi.ini will need to be set up:
# -- Users and Security

Start here:
http://galaxyproject.org/Admin/Get Galaxy

Then see:
http://galaxyproject.org/Admin/Interface
http://galaxyproject.org/Admin/Config/Performance/Production%20Server

The two menu items that are not functioning are covered in the above 
configuration documentation or the universe_wsgi.ini.sample comments.

Hopefully this helps,

Best,

Jen
Galaxy team

On 8/5/11 11:41 AM, sohk...@notes.cc.sunysb.edu wrote:
> Hi,
>
> I have the admin user set in universe_wsgi.ini file, but I am unable to
> login to Galaxy. I get invalid password error.
> In addition, "User" and "Help" menu are not functioning.
> Thanks for any solution.
>
> -Sohail
>
>
> ___
> 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:
>
>http://lists.bx.psu.edu/

-- 
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support

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Re: [galaxy-dev] invalid password

[Jennifer Jackson]

Hello Sohail,

The universe_wsgi.ini for admin is correct. Have you registered through 
the UI yet? Once registered and logged in with these same credentials, 
the account should be granted admin permissions.


Jen

On 8/9/11 11:25 AM, sohk...@notes.cc.sunysb.edu wrote:

Thanks Jennifer,
I login with my e-mail,I have admin_users=my_email and
admin_pass=my_password setup in universe_wsgi.ini. However, I am not
sure if this correct. What is the admin password when you login for the
first time?
-Sohail



From: Jennifer Jackson 
To: sohk...@notes.cc.sunysb.edu
Cc: galaxy-dev@lists.bx.psu.edu
Date: 08/09/2011 02:11 PM
Subject: Re: [galaxy-dev] invalid password




Hello Sohail,

Just as a start, if you have already followed the production server set
up procedures, double check that you are using the email address (and
not the user name) when logging into the UI form.

If that does not solve the admin login issue, is likely that you need to
do some more configuration in the universe_wsgi.ini file. Please see the
sample in your download or at:
http://bitbucket.org/galaxy/galaxy-central/src/1291bc31fec6/universe_wsgi.ini.sample

In particular, this section in universe_wsgi.ini will need to be set up:
# -- Users and Security

Start here:
http://galaxyproject.org/Admin/GetGalaxy

Then see:
http://galaxyproject.org/Admin/Interface
http://galaxyproject.org/Admin/Config/Performance/Production%20Server

The two menu items that are not functioning are covered in the above
configuration documentation or the universe_wsgi.ini.sample comments.

Hopefully this helps,

Best,

Jen
Galaxy team

On 8/5/11 11:41 AM, sohk...@notes.cc.sunysb.edu wrote:
 > Hi,
 >
 > I have the admin user set in universe_wsgi.ini file, but I am unable to
 > login to Galaxy. I get invalid password error.
 > In addition, "User" and "Help" menu are not functioning.
 > Thanks for any solution.
 >
 > -Sohail
 >
 >
 > ___
 > 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:
 >
 > http://lists.bx.psu.edu/

--
Jennifer Jackson
http://usegalaxy.org 
http://galaxyproject.org/Support



--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
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Re: [galaxy-dev] invalid password

[Jennifer Jackson]

Hello Sohail,

Just as a start, if you have already followed the production server set 
up procedures, double check that you are using the email address (and 
not the user name) when logging into the UI form.


If that does not solve the admin login issue, is likely that you need to 
do some more configuration in the universe_wsgi.ini file. Please see the 
sample in your download or at:

http://bitbucket.org/galaxy/galaxy-central/src/1291bc31fec6/universe_wsgi.ini.sample

In particular, this section in universe_wsgi.ini will need to be set up:
# -- Users and Security

Start here:
http://galaxyproject.org/Admin/Get Galaxy

Then see:
http://galaxyproject.org/Admin/Interface
http://galaxyproject.org/Admin/Config/Performance/Production%20Server

The two menu items that are not functioning are covered in the above 
configuration documentation or the universe_wsgi.ini.sample comments.


Hopefully this helps,

Best,

Jen
Galaxy team

On 8/5/11 11:41 AM, sohk...@notes.cc.sunysb.edu wrote:

Hi,

I have the admin user set in universe_wsgi.ini file, but I am unable to
login to Galaxy. I get invalid password error.
In addition, "User" and "Help" menu are not functioning.
Thanks for any solution.

-Sohail


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Re: [galaxy-dev] What happened to 'normal' priority on the issue tracker?

[Jennifer Jackson]

Hi Peter,

The most important part of a ticket is putting clear comments at the 
very top that will help us when we triage, assign, and such. This is 
what we use to adjust the category assignments. Before we triage, the 
assignments are nice, but don't drive project priorities.


So, it is OK leave almost everything as default. In particular, leave 
the state as "new" and responsible as "unassigned" so that we can easily 
locate new tickets.


The form is controlled by the bitbucket team to a large degree, but I'll 
check out the settings anyway to see if something more neutral can be 
made the default. Major for everything new _is_ a bit alarming :)


Thanks!

Jen
Galaxy team

On 8/9/11 2:50 AM, Peter Cock wrote:

Hi all,

I'm just filing a bug on bitbucket, and noticed the default priority
is now major (!)

We can choose: Trivial, Minor, Major, Critical, Blocker

Wasn't there previously a 'Normal' which was the default?

Peter
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Re: [galaxy-dev] Catch problems preparing cluster job scripts

[Jennifer Jackson]

Hi Peter,

On 8/9/11 2:55 AM, Peter Cock wrote:

Hi Jen,




To remind others (readers of this email), bitbucket is not intended to
replace the mailing lists for suspected bugs/bug reports, questions, or
general discussion.
http://galaxyproject.org/Support


Could you clarify that bit on the wiki that reads "If you think you've
seen a bug - please, report it to the Galaxy Development List rather
than the issue tracker", since this seems to requesting email first
rather than filing a bug.


Yes, emailing to the galaxy-...@bx.psu.edu mailing list is the preferred 
way to vet out a potential bug with local or cloud installs Once a 
problem is confirmed, then we can work together to decide if it can 
simply be fixed right away (and by whom) or if it is longer-term issue 
that would be best tracked by opening a ticket.


Thanks for asking - we are working on updating the wiki in this area 
over the next few weeks, so are happy to work together to come up with 
good & clear communication plan. I'll definitely use your comments to 
clarify some of these statements.


Thanks as always Peter!

Jen
Galaxy team



Peter


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Re: [galaxy-dev] [API] About workflow parameters :)

[Jennifer Jackson]

Hello L-A,

On 8/9/11 12:06 AM, Louise-Amélie Schmitt wrote:

Hi Jen,

Hum.. what is a bitbucket ticket? How do you get there?


http://bitbucket.org/galaxy/galaxy-central/src

Tickets are created the same place that the galaxy-central source 
repository is located. Click on the "Issues" tag to see the list of 
requests for enhancements, etc.


It is strongly recommended to get feedback about a request on the 
galaxy-dev list first before opening a bitbucket ticket, to organize 
with the development team here. Your idea seemed like something that 
would be interesting to consider for the primary build, so to keep track 
of it, a ticket would allow both you and our team to track 
status/feedback (better than email, once a specific task is defined). 
Example: submitted patches should get a ticket, followed by an email to 
galaxy-dev with the bitbucket ticket's link and a description of what is 
being offered.


And for others that may be reading this: bitbucket is not the place to 
report bugs. It is also not the correct place to ask a question. Please 
use the mailing lists:

  - galaxy-u...@bx.psu.edu
scientific, data, and tool use discussion
  - galaxy-...@bx.psu.edu
technical problems, local install, cloud, tool/core development
  - if using the public server, submit an error dataset by clicking on 
the green bug icon to reach an internal bug list (data would be private)



There's no real hurry anyway, as far as I'm concerned. I made
API-versions of the tools I need where the python wrapper gets the
needed parameters from a database. But yeah, I'm still very interested
in how the API evolves.

By the way, is there (or will there be) a way to share and delete
histories through the API?


We will have to ask Dannon about that, I'll put him on the cc.

Thanks!!

Jen
Galaxy team



Thanks,
L-A


Le 09/08/2011 02:58, Jennifer Jackson a écrit :

Hi L-A,

Should we make a bitbucket ticket to keep track of this enhancement
request?

If you would like to make one, that would be great since you could put
in all the details, or just write back and I can create a simple ticket.

Thanks!

Jen
Galaxy team

On 8/5/11 6:59 AM, Louise-Amélie Schmitt wrote:

Hello,

Just a quick message to ask if you had the time to work on passing
parameters to workflows through the API. Just to know, since I'm using
workflows with the API.

Best,
L-A
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Re: [galaxy-dev] Tool Config Syntax Wiki page, tag

[Peter Cock]

On Fri, Aug 5, 2011 at 4:19 PM, Jennifer Jackson  wrote:
> Thanks Peter,
>
> The wiki has been corrected, please let us know if you find anything else in
> the current wiki. This was likely from the migration. The next updated
> version of the public wiki is coming soon!
>
> Best,
>
> Jen

Thanks Jen,

I was hoping  or something like that would allow a tool to
set column meta data on tabular output files. Is this possible?

Regards,

Peter
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Re: [galaxy-dev] Catch problems preparing cluster job scripts

[Peter Cock]

Hi Jen,

On Fri, Aug 5, 2011 at 8:27 PM, Jennifer Jackson  wrote:
> Hi Peter,
>
> Yes, if you wanted to create a ticket in bitbucket for this patch that would
> be great. It is the best way to help us to keep track/prioritize. Please
> just submit, but don't change status from "new" or assign to anyone in
> particular. Do feel free to note whether a ticket is intended as a bug
> (fix), enhancement, or proposal.

Done,
https://bitbucket.org/galaxy/galaxy-central/issue/639/catch-problems-preparing-cluster-job

> To remind others (readers of this email), bitbucket is not intended to
> replace the mailing lists for suspected bugs/bug reports, questions, or
> general discussion.
> http://galaxyproject.org/Support

Could you clarify that bit on the wiki that reads "If you think you've
seen a bug - please, report it to the Galaxy Development List rather
than the issue tracker", since this seems to requesting email first
rather than filing a bug.

Peter
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[galaxy-dev] What happened to 'normal' priority on the issue tracker?

[Peter Cock]

Hi all,

I'm just filing a bug on bitbucket, and noticed the default priority
is now major (!)

We can choose: Trivial, Minor, Major, Critical, Blocker

Wasn't there previously a 'Normal' which was the default?

Peter
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Re: [galaxy-dev] suggestion for multithreading

[Louise-Amélie Schmitt]

Well, you still can use my method, which I described at the beginning of 
the thread. But that means modifying some code.


If I'm not mistaken, Galaxy's built-in scheduler is a simple FIFO 
scheduler with no means to tune the needed resources. So if you set 
multithreaded tools, yeah I guess the nodes can expect surprises. That 
could happen with pbs too if you don't set the proper number of needed 
cpu per node / necessary amount of memory.


Or I missed something too.

Best,
L-A


Le 08/08/2011 21:07, Andrew Warren a écrit :
So would the current correct method for setting up multi-threaded jobs 
on a cluster be to specify custom runners in the [galaxy:tool_runners] 
section of the universe config file for EVERY tool that uses a 
multiple threads (assuming the default is set to one)?


For example, for the bowtie program and a queue named "galaxy":
*bowtie = pbs:///galaxy/-l ppn=4,mem=16gb/*
*
*
Is this currently the only way for galaxy to inform the queuing system 
how many threads a program will use?
And does this mean that without custom runners in the config file any 
muti-threaded program that has multiple instances in an asychronous 
workflow has the opportunity to overload a cluster node since the 
queuing system doesn't "know" how many threads the program will be using?


Just want to make sure I'm not missing out on the latest and greatest 
method for process management. :)


Thanks,
Andrew
*
*
Louise-Amélie Schmitt wrote:

> >
> > default_cluster_job_runner will remain for backwards compatibility, 
but

> > we'll ship a sample job_conf.xml that runs everything locally by
> > default.
> >
> > --nate
>
> Haha, and I did that before realizing I could do just what I needed by
> writing tool-specific *pbs*:// URLs at the end of the config file... 
I'm such

> an idiot.

Haha, okay, I don't think i even noticed since I was distracted by your
implementation being a step in the way we want to go with it.

> But I really like what you did of it and I have a couple of questions.
>
> Concerning the single-threaded tools, what would happen if the number of
> threads set in the xml file was >1 ?

It'd consume extra slots, but the tool itself would just run as usual.

> Could it be possible to forbid a tool to run on a given node?

Hrm.  In *PBS* you could do it using node properties/neednodes or 
resource

requirements.  I'd have to think a bit about how to do this in a more
general way in the XML.

--nate

>
> Thanks,
> L-A
>
>
> >
> >>
> >> Peter
> >>


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Re: [galaxy-dev] [API] About workflow parameters :)

[Louise-Amélie Schmitt]

Hi Jen,

Hum.. what is a bitbucket ticket? How do you get there?

There's no real hurry anyway, as far as I'm concerned. I made 
API-versions of the tools I need where the python wrapper gets the 
needed parameters from a database. But yeah, I'm still very interested 
in how the API evolves.


By the way, is there (or will there be) a way to share and delete 
histories through the API?


Thanks,
L-A


Le 09/08/2011 02:58, Jennifer Jackson a écrit :

Hi L-A,

Should we make a bitbucket ticket to keep track of this enhancement 
request?


If you would like to make one, that would be great since you could put 
in all the details, or just write back and I can create a simple ticket.


Thanks!

Jen
Galaxy team

On 8/5/11 6:59 AM, Louise-Amélie Schmitt wrote:

Hello,

Just a quick message to ask if you had the time to work on passing
parameters to workflows through the API. Just to know, since I'm using
workflows with the API.

Best,
L-A
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