Re: [galaxy-dev] API question: is it possible to start exporting histories

[Joachim Jacob | VIB |]

OK, I would like to see that happen too :-)

I have been thinking about possible 'elegant' solutions to enable this 
exporting. I am very enthousiastic about Bittorrent Sync, which could 
perhaps be an efficient and secure way to export the histories 
(http://labs.bittorrent.com/experiments/sync.html). The Galaxy session 
would then show the bittorrent sync 'shared key' in the session, which 
the user can copy paste in their BitTorrent Sync client, after which 
syncing happens. Once syncing is done, connection can quit and exported 
directory deleted from Galaxy. One difficult thing at the client side is 
firewall configuration :-(


Thanks,
Joachim



Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


On 09/06/2013 05:41 PM, Jeremy Goecks wrote:

Is it currently possible to export histories via the API?

Not possible yet but is definitely something we'd like to implement and/or see 
from a community contribution.

Best,
J.



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[galaxy-dev] View Tool Wrapper Code without Installing

[Richard Kuo]

Hello,

Is there a way to see the code for the tool wrappers in the tool shed
without downloading them? I seem to remember that you used to be able to
see the xml and other code before but now it looks like you just have to
install directly from the tool shed.

Thank you,
Richard
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Re: [galaxy-dev] View Tool Wrapper Code without Installing

[Bjoern Gruening]

Hi Richard,

you can navigate to the 'repository actions' -> 'Browse repository tip
files' and have a look at all files in the latest revision of your tool.

Cheers,
Bjoern

> Hello,
> 
> 
> Is there a way to see the code for the tool wrappers in the tool shed
> without downloading them? I seem to remember that you used to be able
> to see the xml and other code before but now it looks like you just
> have to install directly from the tool shed.
> 
> 
> Thank you,
> Richard
> 
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[galaxy-dev] Circumvent "Show all" button

[Gromobir]

Hey guys,
Just one short question: Is there any way to circumvent the "Show all"
dialog within galaxy, if  the data I would like to display is too large?
I would like to display some xhtml files, which can really have a lot of
lines and I don't want the users of my tool to click on this button
every time
before accessing the page. Any hints are highly appreciated.

Best regards,
Gromobir
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[galaxy-dev] Resolving requirement type "binary" and "python-module"

[Hans-philipp Brachvogel]

Hi all,

we run galaxy on a cluster and real user job sumission (via DRMAA).  
The problem is getting the Galaxy standard tools to work with  
environment-module.


We use environment-modules to fit the environment to the needs of a  
job and want to do the same for galaxy jobs. I highly expect the need  
to handle different versions of the same program on our galaxy instance.


It is no problem to configure indivdual evironments for new tools, as  
we can simply set the necessary version="xyz"> entries in the tool.xml and set a 'module load xyz' in  
the corresponding env.sh files.


The challenge is to get the galaxy standard tools to work. Several of  
them do not define a requirement-package tag. Instead one finds the  
types "binary" or "python-module". But these are not handeled by  
Managed Tool Dependencies (env.sh). Especially tools that require  
python-module=rpy, should also have a package=R, or: if  
python-module=Gnuplot I would also need a package='gnuplot' entry to  
trigger the corresponding module load command.


I also found binary=gnuplot, or binary=R... these also need to be  
loaded on our system.


The only way I can think of solving this, is by editing these  
tool.xmls by hand or do you guys think there is a more general  
solution? Are there by chance any methods to resolve binaries and  
python-modules? (could not find anything about it)


Greetings,
Phil
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Re: [galaxy-dev] Resolving requirement type "binary" and "python-module"

[Dave Bouvier]

Phil,

Galaxy uses a number of ways to resolve tool dependencies, some of which 
may be useful in your situation:


1. If a tool dependency entry exists in the database that matches the 
name, type, and version, it attempts to load 
tool_dependency_dir/package_name/version/repository_owner/repository_name/changeset_revision/env.sh


2. If not, it looks for tool_dependency_dir/package_name/version/env.sh 
or tool_dependency_dir/package_name/default/env.sh


3. Even if no env.sh is found in the above steps, it attempts to run the 
command defined by the tool, using executable files from $PATH, python 
modules from the python path, and so on.


If none of the above locations contains the package or module required 
by the tool, it will of course not run successfully.


For more details and step-by-step instructions on configuring your 
Galaxy installation with tool dependencies, see 
http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies


Also, a list of software used by Galaxy standard tools can be found at 
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies


   --Dave B.

On 09/09/2013 10:09 AM, Hans-philipp Brachvogel wrote:

Hi all,

we run galaxy on a cluster and real user job sumission (via DRMAA). The
problem is getting the Galaxy standard tools to work with
environment-module.

We use environment-modules to fit the environment to the needs of a job
and want to do the same for galaxy jobs. I highly expect the need to
handle different versions of the same program on our galaxy instance.

It is no problem to configure indivdual evironments for new tools, as we
can simply set the necessary 
entries in the tool.xml and set a 'module load xyz' in the corresponding
env.sh files.

The challenge is to get the galaxy standard tools to work. Several of
them do not define a requirement-package tag. Instead one finds the
types "binary" or "python-module". But these are not handeled by Managed
Tool Dependencies (env.sh). Especially tools that require
python-module=rpy, should also have a package=R, or: if
python-module=Gnuplot I would also need a package='gnuplot' entry to
trigger the corresponding module load command.

I also found binary=gnuplot, or binary=R... these also need to be loaded
on our system.

The only way I can think of solving this, is by editing these tool.xmls
by hand or do you guys think there is a more general solution? Are there
by chance any methods to resolve binaries and python-modules? (could not
find anything about it)

Greetings,
Phil
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[galaxy-dev] Large files in blend4j

[Eric Kuyt]

Hi all,

I'm using blend4j for some time now and I'm quite happy about it, but
now I run into some OutOfMemory issues.
When I try to upload large files to galaxy (I know http might be not
the best option) some byte array is getting to large. A possible
solution would be file chunking in jersey, is this possible in blend4j
and how could I implement this feature?

Thanks,

Eric

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[galaxy-dev] questions on Galaxy installation under Apache

[Jingchao Zhang]

Hello everyone,

I installed both Galaxy and Apache in a Red Hat linux machine and they work 
fine individually. If I open http://localhost then a welcome page comes out 
showing the httpd is working. In galaxy I changed host=0.0.0.0 and "sh run.sh", 
then the http://localhost:8080 will direct me to the Galaxy 
page.

Now I want to put Galaxy under Apache and here is what I did:
1. First I comment the "host=0.0.0.0" line to stop the build in web server in 
Galaxy and then "sh run.sh" to make Galaxy running.
2. Then I put these lines
RewriteEngine On
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/static/style/(.*) 
/home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/static/scripts/(.*) 
/home/galaxy/galaxy-dist/static/scripts/packed/$1 [L]
RewriteRule ^/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L]
RewriteRule ^/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L]
RewriteRule ^/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L]
RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]
into my "httpd.conf" file. Then I restart the httpd service.

Also, I made changes to the "universe_wsgi.ini" file as instructed and 
restart Galaxy:

[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /galaxy

[app:main]
filter-with = proxy-prefix
cookie_path = /galaxy

After I do these, either http://localhost:8080 nor 
http://localhost/galaxy works. I find two threads talked 
about this problem before:
http://user.list.galaxyproject.org/Installing-galaxy-with-Apache-td4654499.html
http://dev.list.galaxyproject.org/Running-Galaxy-behind-apache2-td4624545.html
but my Red Hat httpd does not has this "/etc/apache2/sites-available/default" 
directory and only has "/etc/httpd/conf/httpd.conf".

Could someone please tell me where should I put those lines in the "httpd.conf" 
file? I have tries various places and none of them works. Any help would be 
deeply appreciated.

Thanks,
Jim
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Re: [galaxy-dev] questions on Galaxy installation under Apache

[Adam Brenner]

Jim,

You need to enable Apache's proxy service. See my pervious post here:
http://dev.list.galaxyproject.org/Running-Galaxy-through-Apache-td4659452.html

Let us know if you run into further issues,
-Adam

--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebre...@uci.edu


On Mon, Sep 9, 2013 at 12:04 PM, Jingchao Zhang  wrote:
> Hello everyone,
>
> I installed both Galaxy and Apache in a Red Hat linux machine and they work
> fine individually. If I open http://localhost then a welcome page comes out
> showing the httpd is working. In galaxy I changed host=0.0.0.0 and "sh
> run.sh", then the http://localhost:8080 will direct me to the Galaxy page.
>
> Now I want to put Galaxy under Apache and here is what I did:
> 1. First I comment the "host=0.0.0.0" line to stop the build in web server
> in Galaxy and then "sh run.sh" to make Galaxy running.
> 2. Then I put these lines
> RewriteEngine On
> RewriteRule ^/galaxy$ /galaxy/ [R]
> RewriteRule ^/static/style/(.*)
> /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]
> RewriteRule ^/static/scripts/(.*)
> /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L]
> RewriteRule ^/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L]
> RewriteRule ^/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico
> [L]
> RewriteRule ^/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L]
> RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]
> into my "httpd.conf" file. Then I restart the httpd service.
>
> Also, I made changes to the "universe_wsgi.ini" file as instructed and
> restart Galaxy:
>
> [filter:proxy-prefix]
> use = egg:PasteDeploy#prefix
> prefix = /galaxy
>
> [app:main]
> filter-with = proxy-prefix
> cookie_path = /galaxy
>
> After I do these, either http://localhost:8080 nor http://localhost/galaxy
> works. I find two threads talked about this problem before:
> http://user.list.galaxyproject.org/Installing-galaxy-with-Apache-td4654499.html
> http://dev.list.galaxyproject.org/Running-Galaxy-behind-apache2-td4624545.html
> but my Red Hat httpd does not has this
> "/etc/apache2/sites-available/default" directory and only has
> "/etc/httpd/conf/httpd.conf".
>
> Could someone please tell me where should I put those lines in the
> "httpd.conf" file? I have tries various places and none of them works. Any
> help would be deeply appreciated.
>
> Thanks,
> Jim
>
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> and other Galaxy lists, please use the interface at:
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>
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Re: [galaxy-dev] Large files in blend4j

[John Chilton]

Glad to hear blend4j is working well, annoyed to here it is not
streaming files out by default.

Based on your ideas I started some work here, but it is not right. I
spent the last half an hour looking around Galaxy trying to figure out
why history creation via the API was broken, not realizing it was
because I called setChunkedEncodingSize on the client.

https://github.com/jmchilton/blend4j/commit/22608de210f805fc192c86a836ea55c7ae1efccf

I have created an issue in github for this:

https://github.com/jmchilton/blend4j/issues/5

Feel free to try to hack on this some more, it might actually take
some non-trivial refactoring to get
client.setChunkedEncodingSize(CHUNKED_ENCODING_SIZE); to be set
conditionally somehow. Right now all requests are sharing the same
underlying client object.

I will try to work on this more as I have time.

-John

On Mon, Sep 9, 2013 at 10:58 AM, Eric Kuyt  wrote:
> Hi all,
>
> I'm using blend4j for some time now and I'm quite happy about it, but
> now I run into some OutOfMemory issues.
> When I try to upload large files to galaxy (I know http might be not
> the best option) some byte array is getting to large. A possible
> solution would be file chunking in jersey, is this possible in blend4j
> and how could I implement this feature?
>
> Thanks,
>
> Eric
>
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