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

[Jennifer Jackson]

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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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
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Re: [galaxy-dev] configuring apache proxy server issue

[Sridhar A Malkaram]

I moved the RewriteRules statements outside the  block
and now it is working.

Thank you.

On Fri, Aug 5, 2011 at 11:57 AM, Assaf Gordon  wrote:

> Your "rewrite" rules are not taking affect (as evident by the fact that
> apache is looking for a folder named "galaxy" in your document root folder
> (/usr/local/apache/htdocs/).
>
> First thing to try is to take the "RewriteRules" statements outside the
> "" block.
>
> Then, enable mod_rewrite logging with the following two statements:
>  RewriteLog /tmp/rewrite.log
>  RewriteLogLevel 9
>
> and restart apache.
> you'll then see every URL access in "/tmp/rewrite.log", and whether
> mod_rewrite handled it or not.
>
> -gordon
>
>
> Jennifer Jackson wrote, On 08/05/2011 11:46 AM:
> > Hello,
> >
> > I am going to move this over to the galaxy-dev list so that the larger
> development community can more easily access your question and provide some
> feedback.
> >
> > Thanks!
> >
> > Jen
> > Galaxy team
> >
> > On 8/4/11 12:55 PM, Sridhar A Malkaram wrote:
> >> Hi,
> >>
> >> I have been using galaxy succesfully for my work using its internal
> >> web-server. Recently I wanted to use it over the internet and so, I
> >> configured it with apache at /galaxy of apache's root. I followed all
> >> the instructions in setting up the proxy redirection. But I think the
> >> re-direction is not happening. I highly appreciate any suggestions to
> >> correct the issue.
> >>
> >> I checked for the mod_proxy, mod_proxy_http etc modules and they are
> >> present and switched on.
> >>
> >> Apache gives the following error in its error_log file:
> >>
> >> [Thu Aug 04 14:15:56 2011] [error] [client 127.0.0.1] File does not
> >> exist: /usr/local/apache/htdocs/galaxy
> >>
> >> Galaxy was set up in the directory /home/galaxy/galaxy-dist
> >> The lines specific for proxy setting in  universe_wsgi.ini  are as
> follows:
> >> use = egg:Paste#http
> >> port = 8080
> >> host = localhost
> >> [filter:proxy-prefix]
> >> use = egg:PasteDeploy#prefix
> >> prefix = /galaxy
> >> [app:main]
> >> filter-with = proxy-prefix
> >> cookie_path = /galaxy
> >> use_remote_user = True
> >> remote_user_maildomain = unl.edu 
> >>
> >> httpd.conf settings:
> >>
> >> RewriteEngine on
> >> http://localhost:8080>
> >> Order deny,allow
> >> Allow from all
> >> 
> >> 
> >> Order deny,allow
> >> Allow from all
> >> # Take the $REMOTE_USER environment variable and set it as a header
> >> in the proxy request.
> >> RewriteCond %{IS_SUBREQ} ^false$
> >> RewriteCond %{LA-U:REMOTE_USER} (.+)
> >> RewriteRule . - [E=RU:%1]
> >> RequestHeader set REMOTE_USER %{RU}e
> >> RequestHeader set X-URL-SCHEME https
> >> RewriteRule ^/galaxy$ /galaxy/ [R]
> >> RewriteRule ^/galaxy/(.*) http://localhost:8080/$1 [P]
> >> # Compress all uncompressed content.
> >> SetOutputFilter DEFLATE
> >> SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip
> dont-vary
> >> SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary
> >> 
> >>
> >>
> >>
> >>
> >> Thanks,
> >>
> >>
> >>
> >> ___
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Re: [galaxy-dev] suggestion for multithreading

[Andrew Warren]

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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